In this work, novel graphene/In2O3 (GR/In2O3) nanocubes were prepared via one-pot solvothermal treatment, reduction reaction, and successive annealing technology at 600 °C step by step. Interestingly, In2O3 with featured cubic morphology was observed to grow on multi-layered graphene nanosheets, forming novel GR/In2O3 nanocubes. The resulting nanocomposites were characterized using transmission electron microscopy (TEM), scanning electron microscopy (SEM), X-ray diffraction spectroscopy (XRD), etc. Further investigations demonstrated that a selective electrochemical sensor based on the prepared GR/In2O3 nanocubes can be achieved. By using the prepared GR/In2O3-based electrochemical sensor, the enantioselective and chem-selective performance, as well as the optimal conditions for L-Lysine detection in Camellia nitidissima Chi, were evaluated. The experimental results revealed that the GR/In2O3 nanocube-based electrochemical sensor showed good chiral recognition features for L-lysine in Camellia nitidissima Chi with a linear range of 0.23–30 μmol·L−1, together with selectivity and anti-interference properties for other different amino acids in Camellia nitidissima Chi.