The unique Karst landforms in Southwest China led to fragile soil structures and erosion, compounded by the large-scale non-agricultural transfer of the rural labor force. This study employed a two-way fixed effects model to analyze the impact of rural labor mobility on the green utilization efficiency of cultivated land, controlling for unobservable individual and time-specific factors. Mediation analysis examined how changes in planting structure influenced this relationship, considering labor force structure heterogeneity. Results revealed a U-shaped relationship, with rural labor mobility initially causing a short-term decline in efficiency but leading to a long-term increase. The mechanism of action showed that rural labor mobility indirectly affected efficiency by altering planting structures; specifically, increased replanting frequency had a partial mediating effect (0.158), while a “grain-oriented” focus masked the effect (0.067). Additionally, an aging workforce and low education levels negatively impacted green utilization efficiency, complicating the situation in the Karst region. To enhance green utilization of cultivated land, it is essential to protect migrant farmers’ rights, improve agricultural labor quality, promote industrial upgrades, and adjust planting structures. These strategies will guide regional agriculture and ensure sustainable land resource use.