This paper reveals the mechanisms by which the spatial structure of morphological polycentricity (MP) affects the subjective well-being (SWB) in China, focusing on the distribution of economic activities. Using panel data for 21 provinces in China from 2010 to 2020, we compare the effects of dynamic MP, measured using nighttime light data, and static MP, measured using demographic data, on SWB. Our findings reveal that, as regional economic benefits enhance and megacities form, the adjustment of MP spatial policy becomes increasingly significant in improving SWB. Notably, dynamic changes in MP exhibit a more pronounced effect on the satisfaction and confidence aspects of SWB. Moreover, increased urban-rural income inequality moderates this relationship, diminishing the positive impact of MP on SWB among rural households. Regional analysis indicates that in economically advancing areas and emerging megacities, adjustments in MP spatial policy are increasingly crucial for improving SWB. Central regions experiencing economic growth exhibit a greater need to balance economic agglomeration with population dispersion to optimize well-being outcomes. The empirical evidence provided suggests the potential benefits of adopting harmonized development strategies and indicates that incorporating the socio-economic context into spatial planning may contribute to the optimization of well-being. • Dynamic morphological polycentricity (MP) has a stronger positive effect on subjective well-being (SWB) than static MP, highlighting the importance of accounting for economic dynamics in the study of geographical well-being. • Urban-rural income inequality weakens the positive effect of MP on SWB, emphasizing that optimizing spatial structures in isolation is insufficient for substantially enhancing residents' SWB; social-economic inequalities must also be addressed collectively. • Regional economic heterogeneity significantly influences the effect of MP on SWB, and MP policies should prioritize the eastern regions, while the central regions require greater focus on balancing economic agglomeration and population dispersion.