The Under-20 boss replaces Gareth Southgate, who will look after the senior team for their next four matches after the departure of Sam Allardyce.
A point in Kazakhstan on 6 October will be enough for the Under-21s to secure a spot in next year's finals in Poland.
Their final group match is at home to Bosnia and Herzegovina.
Boothroyd's assistant coach Paul Williams will take charge of the Under-20s on an interim basis.
Boothroyd has coached the England Under-20 side since 2014.
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This species is well-known for its clever tool tricks, but studying its behaviour in the wild is difficult.
These tiny cameras peer forwards beneath the birds' bellies and record precious, uninhibited footage.
As well as glimpsing two crows making special foraging hooks, the team was able to track their activity over time.
This "activity budget" offers a rare insight into the natural lives of New Caledonian crows - but it has not yet solved the mystery of precisely what drives these birds to use tools.
That is the "big money question" according to senior author Christian Rutz, from the University of St Andrews in the UK.
"Why is it that New Caledonian crows use tools but other corvids don't? I think the answer to that lies in looking at their time budgets and figuring out how important tool use is in their everyday lives - what kinds of prey sources they tackle with tools," Dr Rutz told the BBC.
In nearly 12 hours of "crow cam" footage from 10 different birds, described in the journal Biology Letters, he and his team actually caught surprisingly little tool time on camera.
"Out of total observation time, only about 3% was spent making or using tools," Dr Rutz said. And only four of the 10 subjects picked up a tool at all.
Instead, the crows spent considerably more time foraging with their beaks. And when one of the four tool-users did reach for a twig, the decision was often rather baffling.
For example, the birds spent a lot of time tearing strips from paperbark trees in search of grubs. Their sturdy beaks are perfectly good for this task.
"But every now and then, they suddenly switch into tool use - in the very same trees, in a very similar foraging context," Dr Rutz said. "We don't understand what is happening there."
Meanwhile, there were two moments in particular that made the team, sifting through hours of shaky crow-cam video, very happy indeed.
Two different crows filmed themselves not just wielding sticks but making - and using - hooks: a known party trick of New Caledonian crows, never before caught on video except in cages or at baited feeding sites.
"When we got that footage it was a proper high-five moment in the field camp," Dr Rutz said.
From lab experiments and previous brief sightings through binoculars, the team knew that the birds made these hooks. They snap off one branch from a forked twig and leave a small part of the main stem attached to the end.
But now they had video evidence of it happening unprompted, in the wild.
"We were keen to get close-up video of birds making these tools under completely natural conditions," said  co-author Jolyon Troscianko from the University of Exeter.
"New Caledonian crows are notoriously difficult to observe, not just because of the challenging terrain of their tropical habitats, but also because they can be quite sensitive to disturbance."
Key to the research effort, funded by the Biotechnology and Biological Sciences Research Council, was a new design for the team's crow cam system.
Instead of beaming the video to a receiver in the field, which had previously seen researchers scrambling through the New Caledonian forest with antennas, these devices stored the footage on a micro SD card.
Then, after about a week, the gadgets fell off the birds and the team tracked them down thanks to a tiny radio beacon.
"We got much longer, uninterrupted video recordings," Dr Rutz said.
"We were lucky that we recorded the hook tool makingâ€¦ but we also got enough data to look at energy budgets and so on. That kind of data is gold dust for us."
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Former Watford and Coventry manager Aidy Boothroyd will take charge of the England Under-21 team for their final two Euro 2017 qualifiers.
[NEXT_CONCEPT]
Ecologists have used a tail-mounted "crow cam" to catch wild New Caledonian crows in the act of making and using hook-shaped tools.