Based on the theories of structure–function correlation in Geography, and landscape pattern-ecological function correlation in Landscape Ecology, the correlation between land use fragmentation and vegetation activity was quantified. Effective mesh size (meff) was calculated to represent landscape fragmentation for land use, and the normalized difference vegetation index (NDVI) was used to reflect vegetation activity. The geographically weighted regression (GWR) model was applied to explore the spatial non-stationary relationship between meff and NDVI in a karst basin of the southwestern China, where environmental factors (i.e., climate, topography, and vegetation) are spatially heterogeneous. The spatial variation and scale dependence of landscape fragmentation and its relationship with vegetation activity, as well as the influence of lithology types and landforms relief, were considered. Firstly, the optimal ‘slide window’ size for landscape fragmentation was determined to be 500 m, and spatial pattern of meff displayed clear heterogeneity with a serious degree of fragmentation. Landscape fragmentation was more severe in carbonate areas than non-carbonate areas, reflecting the influence of landforms relief. More serious fragmentation in dolomite areas meant that the impact of human activities on the landscape morphological characteristics was much more significant than that in the limestone areas with steeper slope. Multi-scale analysis was used to verify a neighborhood size of 7 km for GWR in the study area. Negative effects on vegetation activity from landscape structural changes were more significant in limestone areas, which may be due to the more vulnerable ecosystems there. This research can provide scientific guidance for landscape management in karst regions as it considers the multi-scaled and spatially heterogeneous effects of lithology, geomorphology, and human factors on landscape structure and its correlation with vegetation activity.