Developing advanced anode materials is essential for enhancing the rate performance and stability of lithium-ion batteries (LIBs), which is critical for meeting the demands for next-generation energy storage solutions. In this research, Cu2SnS3/rGO nanocomposites were synthesized via a rapid microwave-assisted one-step method, followed by post-synthetic annealing. The incorporation of reduced graphene oxide (rGO) not only significantly improves its electrical conductivity, but also effectively inhibits the agglomeration of CTS nanoparticles. The nanocrystal size in the CTS/rGO nanocomposites has been dramatically downsized, transitioning from the pristine CTS dimensions of 0.9–1.5 μm to a mere 100 nm. This downsizing is a critical advancement in the electrode, as it enhances the surface area and reactivity of the composite. The subsequent high-temperature annealing process shrinks the pore size in the CTS/rGO nanocomposite, decreasing from an average of 42.13 nm to a more confined range of 7.81 to 8.77 nm, depending on the annealing temperatures. Electrochemical testing reveals that the CTS/rGO-A nanocomposite annealed at 300 °C exhibits superior electrochemical performance to the unmodified CTS and non-annealed CTS/rGO composite. The performance is evidenced by an initial capacity of 1856.97 mAh g−1 at a current density of 1 A g−1 and retains a capacity of 1250.32 mAh g−1 after 500 cycles. To elucidate the underlying mechanisms governing the lithium ion diffusion kinetics, capacitance and diffusion behavior of the CTS/rGO-A electrode, advanced techniques such as galvanostatic intermittent titration technique (GITT) and rate cyclic voltammetry (CV) were utilized. These analyses revealed that the synergistic effect of an increased Li+ diffusion coefficient (DLi+), coupled with a notable capacitive contribution, is demonstrated to the enhanced electrochemical performance observed. Furthermore, the COMSOL Multiphysics simulation also indicates improved structural stability of CTS/rGO-A, attributed to minimized stress from volume expansion during discharge. The CTS/rGO-A nanocomposites, featuring enhanced electrochemical performance, coupled with a straightforward and efficient fabrication method, emerge as a promising material for scalable and practical energy storage solutions.