Most developed megacities have experienced poly-centralization and suburbanization, leading to job-housing mismatches and negative outcomes such as increased commuting distances and frequencies. Recognizing the scarcity of structural analysis concerning the attractiveness of commuting's geographic endpoints, this study examines the diverse impact of the built environment at living and working locations on commuting flows, considering various supply-demand masses and distance levels. Utilizing a Gradient Boosting Decision Tree (GBDT) model, the study highlights the importance of job-housing ratio, POI diversity, and subway station proximity in employment locations, while informal area rates and subway proximity remain significant in residential locations. A three-dimensional analysis further indicates that achieving a perfect job-housing balance in megacities remains a dream, with each area presenting unique challenges requiring tailored solutions beyond a one-size-fits-all approach. Potential policies, such as planning large residential areas in the inner suburbs and upgrading convenient infrastructure in the outer suburbs, are proposed. Furthermore, with the uncovered distinct interaction effects of built environment on commuting behavior across various masses and distances, common perceptions related to mixed-use land and the role of informal settlement, are critically challenged. This extends our understanding of sustainable urban system design and provides references for planning policies.