A well-controlled chemical synthetic protocol was developed to prepare a novel conductive, polypyrrole (PPy)/cellulose nanocrystal (CNC) system that is simple, cost-effective and scalable. Carboxylic acid groups were grafted onto CNC via a TEMPO-mediated oxidation providing strong hydrogen bonding to enhance adsorption of pyrrole monomers (Py). In-situ chemical polymerization of Py was further performed on a single high aspect ratio CNC. The nanotemplating of CNC controlled the deposition and growth of the polymer layer, which enhanced the electrochemical properties of PPy. Improved processibility of PPy was achieved due to the high mechanical strength and good dispersibility of CNC. By varying the ratio of Py to surface hydroxyl groups of CNCs (Py/OH) systematically, an optimal composition of Py/OH of 16:1 was observed. The mechanism of the electrochemical performance change associated with Py/OH molar feeding ratio was also studied in detail using different spectrometry and SEM methods. PPy/CNC hybrid nanostructures possessed an attractive specific capacitance of 248 F g−1, suitable for supercapacitor applications and exceeding the performance of comparable systems based on carbon nanotubes and graphenes. Compared with other cellulose-polypyrrole systems whose end-products are typically entangled fiber mat, aerogel or cake-form, our CNC nanorods can be readily dispersed and added as fillers into different matrices. The PPy/CNC hybrid nanostructure is extremely light, conductive, cheap, renewable, environmentally friendly, and our solution-phase chemical synthesis is simple to implement and easy to scale up.