This study combined a reach-scale field survey and numerical modelling analysis to reveal the pattern of transient hyporheic exchange driven by rainfall events in the Zhongtian River, Southeast China. Field observations revealed hydrodynamic properties and flux variations in surface water (SW)/ groundwater (GW), suggesting that the regional groundwater recharged the study reach. A two-step numerical modelling procedure, including a hydraulic surface flow model and a groundwater flow model, was then used to interpret the transient hyporheic flow system. The hyporheic exchange exhibited strong temporal evolution in the study reach, as indicated by the rainfall event-driven hyporheic exchange. The reversal of the hydraulic gradient and transient hyporheic exchange were simulated using numerical simulation. Anisotropic hydraulic conductivity is the key to generating transient hyporheic exchange. A revised conceptual model was used to interpret the observed temporal patterns in hyporheic exchange. The seasonal rainfall events generate transient hyporheic exchange, and the pattern of transient hyporheic exchange indicates that transient hyporheic exchange appears only after an increased phase of the river stage but does not last long. The temporal pattern of hyporheic exchange can significantly affect the hydrodynamic exchange and the evolution of hydrology in the hyporheic zone for a gaining stream, and these results have important guiding significance for the comprehensive management of surface water and groundwater quantity and quality.