The isotopic composition of atmospheric species provides fundamental insights into their sources, sinks, and chemical processes. However, conventional end-member mixing box models fail to accurately represent the progressive isotopic evolution within complex systems, where mixing and reactions occur simultaneously. This limitation hinders a comprehensive understanding of the isotope effect and its atmospheric applications. To address this, we have designed an isotopic chemistry module and incorporated it into the three-dimensional chemical transport model, using an iterative time-splitting method to reduce bias introduced by the Rayleigh equation. The model incorporates four isotopologues (³²SO₂, ³⁴SO₂, ³²SO₄²⁻, ³⁴SO₄²⁻) as prognostic tracers for SO₂ and sulfate aerosol, simulating isotope effects during various gas-phase, heterogeneous/multiphase and aqueous-phase reactions. Validation against compiled observation data demonstrates the model's ability to reproduce the sulfur isotope effect (Δδ³⁴S_SO₄²⁻/SO₂= 3.43±1.11‰) and spatiotemporal variations of δ³⁴SO₄²⁻ across Eastern China. Further, our study underscores the importance of considering isotopic fractionation during combustion and chemical processes for accurate source apportionment using the isotope mixing model. The isotope-enable model presents an innovative approach for effectively constraining the sulfur budget.