We report a low temperature facile approach to control the nanostructure morphologies of molybdenum oxide (MoO3) for high performance lithium ion batteries (LIBs). Nanorods and nanoflowers of MoO3 can be obtained by simply controlling the acidity of the precursor solution during sonication. We have found that the nanostructures play a key role in determining the performance of LIBs. Particularly, the LIB with MoO3 nanoflowers as the anode can achieve a specific capacity up to 1020mAhg−1 at a discharge current density of 550mAg−1. This capacity is close to the theoretical limit and is among the highest reported with MoO3-based anodes, it suggests the nanostructures is efficient for ion intercalation during the charge and discharge processes. The LIBs using the MoO3 nanoflower anode also show superior cycling performance; 78% of the maximum capacity can be retained even after 100 charge/discharge cycles. Since the presented low-cost and simple synthesis approach can be easily implemented in large scale, it has a large potential for the application of high performance lithium ion batteries.