Abstract This study took the Meijiang River Basin, China as an example, to simulate the resilience interactions of three key subsystems of land, water and biodiversity from 2000 to 2015, using a spatially explicit model. Twelve environmental variables were selected from natural, landscape pattern and socioeconomic dimensions to detect the dominant factors of system resilience interactions using a geographic detector model. We found that the resilience of water yield, soil retention and biodiversity were mainly influenced by landscape pattern factors. Additionally, terrain is a main driver of soil retention resilience, precipitation plays a critical role influencing water yield resilience variations and biodiversity resilience variations remains stable influenced by landscape pattern. Larger synergy and loss occurred between water yield resilience and biodiversity resilience compared with other pairs of resilience, while greater tradeoffs occurred between soil retention resilience and biodiversity resilience. The interactions among landscape pattern, precipitation, terrain and GDP were main driving forces of land and water resilience interactions. The interactions of landscape pattern, terrain were main driving forces of land and biodiversity resilience interactions. The interactions of landscape pattern, precipitation and GDP were main driving forces of water and biodiversity resilience interactions. Our study implied that improving habitat connectivity could maximize benefits.