Identifying and evaluating polycentric urban spatial structure is essential for understanding and optimizing current urban development. In order to accurately identify the urban centers of the Guangdong–Hong Kong–Macao Greater Bay Area (GBA), this study firstly fused nighttime light data, POI data, and population migration data based on wavelet transform, then identified the polycentric spatial structure of the GBA by carrying out cluster and outlier analysis, and evaluated the level of different urban centers byconducting geographical weighted regression analysis. Using data fusion, we identified 4579.81 km² of the urban poly-center area in the GBA, with an identification accuracy of 93.22%. Although the number and spatial extent of the identified urban poly-centers are consistent with the GBA development plan outline, the poly-center level evaluation results are inconsistent with the development plan, which shows there are great differences in actual development levels among different cities in the GBA. By identifying and grading the polycentric spatial structure of the GBA, this study accurately analyzed the current spatial distribution and could provide policy implications for the GBA’s future development and planning.