Population, resource, environment and development (PRED) is a focus question of human-earth relationship and an everlasting subject of geographic research. The theory of synergism of five rules in PRED and conceptual mathematical model of PRED evolution trajectory were analyzed, then the controlling macro-model of integration of six factors and its grey index assessment system in bay area were proposed whereby. Also the regulation programs for PRED of bay area evolved in a well-ordered way was devised. The synergism of five rules, refers to the coupling of natural rule, social rule, economic rule, environmental rule and technical rule. The integration of six factors means organizing of ecotype, safety, health, landscaping, culture and profit. The reciprocity of synergism of five rules and integration of six factors is interdependent. Take the Xiamen Bay as an example. The city of Xiamen has reached a highly developed stage, whose first industry has nearly been replaced by the secondary and tertiary industries, but oceanic species like Chinese dolphin, lancelet, etc. and mangrove wetland were preserved. The grey assessment result of integration of six factors is 75.725, indicating that main limiting factors of PRED in the Xiamen Bay are artificial coastline, seawater pollution and shipping channel siltation. The focus of PRED regulation should be: protect coastal eco-source, prevent port and shipping channel from silting, curtail pollution from land, improve landscape of coastline and islands, keep the predominance of sea transportation industry and travel industry and expand to new & high-tech oceanic industries. The study shows that the theory of synergism of five rules and integration of six factors brings a general idea and oriental guide for PRED in bay area, and planning foreseeingly on resource utilization and environmental protection is an exercisable controlling means. Based on the continually comparison and adjustment of six factors among several representative bays, each factor of PRED will keep in a well-ordered way, the conceptual mathematical curve of PRED evolution trajectory will keep ascending, and the distinction of PRED of each bay will be revealed.