Developing high-performance anode materials is a crucial research target of sodium-ion batteries (SIBs). Transition metal oxides (TMOs) have attracted great interest as potential anodes, but their applications are still hindered by slow reaction kinetics and large volume changes. Herein, Mo-aniline nanorods (Mo-ANRs) are prepared as precursors by a simple self-polymerized method in acid condition. After the in-situ phase transformation during annealing, multistage composites (N-CNRs@g-MoO2) are formed, with N-doped carbon nanorods (N-CNRs) converted from polymeric aniline ligands, on which granular molybdenum dioxide (g-MoO2) are uniformly precipitated and residual MoO2 nanodots are remained. As anode materials for SIBs, N-CNRs@g-MoO2 electrode is benefited from the shortened ion/electron diffusion length caused by steady g-MoO2 and residual nanodots, and the enhanced electrical conductivity and relieved volume changes introduced by N-CNRs and unique architecture. Thus, N-CNRs@g-MoO2 electrode delivers high discharge capacity (497.5 mAh g−1 at 0.05 A g−1), excellent rate performance and ultra-long cycling stability (165.6 mAh g−1 at 10.0 A g−1 after 12000 cycles), and 122% capacity retention is obtained at 1.0 A g−1 over 500 cycles even after the rate test. The significant enhancements in sodium-ion storage are mainly attributed to the multistage architecture and synergistic advantages among MoO2 nanodots, N-CNRs and g-MoO2. These results indicate that the in-situ phase transformation route has great potential in constructing novel composites with unique architecture for high-performance SIBs.