Isoprene-derived secondary organic aerosol (ISOA) is an important component of atmospheric organic aerosol, but its formation remains incompletely represented in global chemical models, creating uncertainty in ISOA changes and their drivers. In this study, we updated the explicit isoprene chemistry scheme in Community Atmosphere Model version 6 with comprehensive tropospheric and stratospheric chemistry (CAM6-Chem) by adding isoprene epoxydiols reactive uptake to aerosol liquid water under low-NOx conditions and key gas-phase precursors and subsequent heterogeneous processes under high-NOx conditions. Evaluation against ground-based observations shows that the updated model better reproduces the concentrations and compositional structure of four ISOA subspecies, rather than only one in the default model. At the bulk aerosol level, the update alleviates the underestimation of SOA over China, improving normalized mean bias from −76.7 % to −50.0 %. ISOA formation in China is governed by NOx-dependent competition between the low- and high-NOx pathways, with the former remaining dominant at the national scale. Long-term analysis for 2000–2019 shows a weak national-mean ISOA trend due to offsetting regional changes of opposite signs. The most pronounced increase occurs in Southwest China, where enhanced biogenic isoprene emissions account for 61.92 % of ISOA increase, whereas the strongest decrease occurs in the Shaanxi–Gansu–Ningxia region, where increasing anthropogenic nitrogen oxides (NOx) emissions and declining sulfate account for 48.96 % and 45.11 % of the decrease, respectively. These results highlight the regional heterogeneity of ISOA changes in China and the importance of jointly representing precursor supply and heterogeneous reaction conditions in simulating ISOA formation and trends.