In turbid macro-tidal estuaries (MTE), typhoons interact with tides and high turbidity, significantly impacting the natural and social environments of the coastal zones. Understanding the suspended sediment fluxes (SSF) and their mechanisms in macro-tidal turbid estuaries during typhoons is therefore crucial. In this study, a tide-wave-sediment numerical model was built and validated for Hangzhou Bay (HZB), using Typhoon Chan-hom as a case study. The model incorporates an optimized near-shore typhoon wind field, wave-current coupling, water-sediment density coupling, and sediment flocculation. The bottom boundary layer for fluid mud was also considered in the model. Results show that residual currents were stronger near the southern bank than the northern bank, converging on the southern bank before flowing to the open sea during the typhoon. The direction of the net SSF in the bay was from north to south. Increased wave-induced bottom stress led to intensified sediment resuspension, subsequently increasing suspended sediment concentration (SSC) and SSF during the typhoon. Typhoon wind fields primarily governed sediment transport, with great wave impacts on both the south and north banks, while the effect of air pressure was negligible. Residual currents and SSC were positively correlated with typhoon intensity. More so, tide-surge nonlinear effects inhibited the increase of SSC. The nonlinear residual currents at the bay mouth flowed from south to north, and the nonlinear suspended sediment was brought into the bay from the open sea. Euler residual currents (T1) and sedimentation and resuspension (T4) were the main drivers of sediment transport during the typhoon. Wind field, waves, air pressure, and nonlinear effects also influence SSF, mainly by affecting T1 and T4. This study’s findings show the correlation between typhoons and sediment fluxes in macro-tidal turbid estuaries, providing valuable insights for coastal zone management.