The Pearl River Delta (the PRD) is a strategic region for China’s development. Since the Reform and Opening up of China in 1983, the PRD has been growing from several isolated cities to one megacity region. Uncovering spatial characteristics is essential for the megacity region synergy, regional planning, and governance. Massive mobile phone location data contains hidden information of complex spatial networks. From the flow perspective, this study thereafter constructs a large-scale mobility network using long-period mobile phone location data. The Louvain method is adopted to detect spatial communities, which reveals the spatial cooperation within the detected area. The disparity filter is used to extract the backbone network, which unravels the geographical connection among these areas. An experiment in the PRD was conducted to investigate the spatial synergy in the PRD. The results suggest that the PRD is with a significant trend of spatial synergy; the backbone of mobility network demonstrates that Guangzhou and Shenzhen are the spatial cores; the East-West differences do exist, the closer to the central urban areas, the higher the degrees of spatial integration. These results will benefit the synergic spatial planning and governance of the PRD.