Urban spatial expansion (USE) is an uneven process affected by both natural and human factors, and land use regulation policy is of significance. To indicate the potential effects of different policies at a regional scale and then improving them under the context of increasing emphasis on land protection, we take Southern Jiangsu Urban Agglomeration (SJUA) in eastern China as a case study. Based on USE simulation with a minimum cumulative resistance (MCR) model under four scenarios related with arable and ecological land protection, we analyze the spatial differentiation of newly added urban construction lands and examine the changes of urban system with fractal analysis. Results indicate the allocations of newly added urban construction land differs by scenarios as well as total expanding amounts, and larger cities tend to grow faster. The share of the four largest cities (Suzhou, Nanjing(S), Wuxi, and Changzhou) were mostly higher than 40%. Accordingly, the final area of all cities was linearly corrected with their extant sizes in 2010. However, the differentiated allocations of newly added urban lands related to both increasing expanding amounts and different scenarios caused differences in the said linear relationships and also influenced urban rank-size in different degrees. It is concluded that the MCR model is feasible for simulating regional scale urban expansion and land protection strategies do not induce dramatic changes to the basic structures of regional urban system, but they are slightly different as land protection strategies change. The spatial distribution of protected lands affect the differentiation of both the predicted expanding amount of different cities and the regional urban systems significantly. It is of importance to optimize the spatial distribution of protected lands to regulate regional scale USE patterns and also urban systems properly.