Urban spaces, though often perceived as discrete communities, are shared by various functional and social groups. Our study introduces a graph-based physics-aware deep learning framework, illuminating the intricate overlapping nature inherent in urban communities. Through analysis of individual mobile phone positioning data at Twin Cities metro area (TCMA) in Minnesota, USA, our findings reveal that 95.7 % of urban functional complexity stems from the overlapping structure of communities during weekdays. Significantly, our research not only quantifies these overlaps but also reveals their compelling correlations with income and racial indicators, unraveling the complex segregation patterns in U.S. cities. As the first to elucidate the overlapping nature of urban communities, this work offers a unique geospatial perspective on looking at urban structures, highlighting the nuanced interplay of socioeconomic dynamics within cities.