Urban agglomeration is an important spatial organization mode in China’s attempts to attain an advanced (mature) stage of urbanization, and to understand its consequences, accurate simulation scenarios are needed. Compared to traditional urban growth simulations, which operate on the scale of a single city, urban agglomeration considers interactions among multiple cities. In this study, we combined a spatial Markov chain (SMC) (a quantitative composition module) with geographically weighted regression-based cellular automata (GWRCA) (a spatial allocation module) to predict urban growth in the Guangdong–Hong Kong–Macao Greater Bay Area (GBA), an internationally important urban agglomeration in southern China. The SMC method improves on the traditional Markov chain technique by taking into account the interaction and influence between each city to predict growth quantitatively, whereas the geographically weighted regression (GWR) gives an empirical estimate of urban growth suitability based on geospatial differentiation on the scale of an urban agglomeration. Using the SMC model to forecast growth in the GBA in the year 2050, our results indicated that the rate of smaller cities will increase, while that of larger cities will slow down. The coastal belt in the core areas of the GBA as well as the region’s peripheral cities are most likely to be areas of development by 2050, while established cities such as Shenzhen and Dongguan will no longer experience rapid expansion. Compared with traditional simulation models, the SMC-GWRCA was able to consider spatiotemporal interactions among cities when forecasting changes to a large region like the GBA. This study put forward a development scenario for the GBA for 2050 on the scale of an urban agglomeration to provide a more credible scenario for spatial planning. It also provided evidence in support of using integrated SMC-GWRCA models, which, we maintain, offer a more efficient approach for simulating urban agglomeration development than do traditional methods.