Fissures and conduits are main void of karstic aquifer. Karst aquifers are highly vulnerable to contamination as water exchange between fissure system and conduit system greatly influences the karstification of limestone terrains, heterogeneity of karstic aquifer, and spring flow regime. A two-dimensional tank model was constructed, and a corresponding numerical model (MODFLOW-2005 Conduit Flow Process Mode 1, CFPM1) was developed to explore the effects of rainfall intensity and intrinsic structure of karst system (hydraulic conductivity of fissures and conduit diameter) on conduit-matrix water exchange. Nine different scenarios were designed to quantitatively simulate the spatial and temporal variability of water exchange between the fissures and conduits. The study reproduced the area of fissure water recharging to conduit (recharge zone), the area of conduit water discharging to fissure water (discharge zone) and the area of fissure water moving laterally (transport zone) in both physical model and numerical model. The results from rainfall scenarios show a relatively stable ratio of exchange zone (recharge zone and discharge zone) with increasing rainfall intensity, indicating that conduit-matrix water exchange is not sensitive to rainfall intensity, and conduit water discharging to fissure water is just a short-term phenomenon. It is also found that an increase in hydraulic conductivity of fissure system enhances extensiveness of water transport, but restrains conduit-matrix water exchange. However, the enlargement of conduit can prompt the extent of conduit-matrix water exchange. A positive feedback between the extent of conduit-matrix water exchanges and karstification can be confirmed. These findings might be essential for better understanding groundwater flow dynamics in karst aquifers.