SnO2 as a promising anode material possesses a high theoretical capacity and a safe lithiation potential; however, it suffers from low cycle stability and poor rate capability due to its nano-aggregation effect, structural instability, and sluggish electrode kinetics. Herein a one-pot hydrothermal process was developed to craft ultrasmall SnO2 nanocrystals uniformly encapsulated in the polyimide matrix through a facile in-situ polymerization. The polyimide phase can suppress the over growth of SnO2 nanoparticles while preventing from their re-aggregation through the space-confined effect during the material synthesis. The robust polyimide matrix can be also served as a protective layer to relieve the volume change of SnO2 nanoparticles and inhibit the cracks propagation throughout the whole electrode during the charge/discharge processes. Moreover, the carbonyl-contained polyimide is intrinsically redox-active, capable of affording acceptable ionic conduction ability. Remarkably, the as-fabricated SnO2@PI composite anode exhibits a reversible capacity as high as 897 mAh g−1 at 0.1 A g−1 and a high rate capability (479 mAh g−1 at 2.0 A g−1) with a higher retention (53%) than pure SnO2 (39%). The SnO2@PI anode also retains a capacity of 653 mAh g−1 at 0.5 A g−1 after 150 cycles. This work would offer an alternative strategy by incorporating metal oxide nanoparticles into the redox-active polymer matrix for advanced anode materials with high rate capability and long-term cyclability.