Cultivated land intensive utilization (CLIU) exhibits spatial heterogeneity that is influenced by both natural and anthropogenic factors, with land dissected into different scale systems; however, CLIU has not yet been systematically explored. This study takes the Beibu Gulf urban agglomeration, a national-level model area for integrated land and sea development in China, as an example to investigate the spatial heterogeneity of CLIU and explore its driving factors through multiple econometrical and geographical methods, including identifying its underlying mechanisms. The results indicate that (1) the CLIU index is 0.334, its Gini coefficient is 0.183, and its comprehensive level has a low intensity and obvious spatial nonequilibrium characteristics. Hypervariable density (50.33%) and the intraprovincial gap (45.6%) are the main sources. (2) Among the independent effects of single factors, the multiple cropping index (0.57), labor force index (0.489), and intensification of construction land (0.375) exert the most influence on CLIU spatial variation. The interaction effects of two factors primarily manifested as nonlinear enhancements, with the interaction between the labor force index and multiple cropping index being particularly noteworthy (0.859). (3) The geographically weighted regression coefficients reveal that temperature (0.332), multiple cropping index (0.211), and labor force index (0.209) have relatively large and positive impacts on CLIU, while slope (−0.1), precipitation (−0.087), and population urbanization (−0.039) have relatively small and negative impacts; all factors exhibit spatial nonstationarity. The spatial heterogeneity of CLIU in the Beibu Gulf urban agglomeration is characterized by patterns’ nonequilibrium and factors’ nonstationarity. The driving mode of multiple factors on CLIU is manifested as follows: natural factors of cropland utilization provide basic guarantees, internal factors of CLIU provide positive enhancement, and external factors of land intensive utilization provide auxiliary promotion.