<p>Urban form exerts asymmetric influences on environmental outcomes, posing complex trade-offs for spatial governance. This study identifies and conceptualizes a “Pollutant’s Dilemma” within the Beijing–Tianjin–Hebei urban agglomeration, wherein urban concentration simultaneously intensifies PM_2.5 emissions through agglomeration effects and reduces CO₂ emissions via intensification. Using 5-km grid data for three structurally significant time points—2014 (policy baseline), 2018 (structural restructuring phase), and 2022 (transition endpoint)—we develop a novel analytical framework that couples Stacking ensemble learning with Shapley Additive Explanations (SHAP) interpretation to uncover both dominant and interaction effects of urban form. The analysis yields three principal findings. First, urban concentration exerts opposing effects on the two pollutants—amplifying PM_2.5 via agglomeration while suppressing CO₂ via intensification—with a population density threshold of approximately 600 persons·km⁻² marking the critical governance inflection point. Second, PM_2.5 drivers follow a coherent three-stage evolutionary trajectory (from “ecological dependency” through “scale-ecology trade-off” to “efficiency-balancing”), whereas CO₂ drivers exhibit persistent structural lock-in dominated by economic and built-up scale throughout. Third, High-High clusters embody the Dilemma in its mature form—with antagonistic multi-factor PM_2.5 regulation co-existing alongside unidirectional scale-driven CO₂ promotion—while Low-Low clusters represent a “pre-dilemma” state governed by morphological and ecological mechanisms. These findings challenge the pro-density planning paradigm and provide a stage-sensitive empirical basis for integrating spatial planning with climate mitigation and public health objectives in rapidly urbanizing megaregions.</p>