This study aimed to: (i) characterize the runoff pollution before and after urbanization; (ii) analyze the cost-effectiveness of different GI strategies and their combinations (CGIs); and (iii) provide the scientific basis for Multi-Objective Decision-Making for the Sponge City planning. Using the rapidly developing Western New City of Zhuhai as the case study, we analyzed the characteristics of the current urban rainfall-runoff pollution and the changes of pollution load before and after planning through field monitoring. To evaluate the performance and cost-effectiveness, six GI and CGI scenarios were considered with the use of SWMM modeling. The results indicated that: (1) under the current condition, heavy runoff pollution (inferior to water quality class V) was identified for roads and paved ground in the developed areas; (2) there existed obvious initial flush effect from roofs and ground; (3) after development, the runoff pollutant loads were 2.9~3.2 times as those under current conditions; (4) the CGI (source/source-terminal controls) yielded better overall performance than the single GIs, however its cost per unit of pollutant reduction was higher; (5) among the single GIs, the detention basin yielded the lowest cost per unit of reduction, and it also effectively reduced TN and TP; (6) bio-retention and vegetated swale also yielded low reduction cost, but they could not effectively reduce the pollutant load; and (7) the reduction cost per unit of permeable pavement is the most expensive among all considered single GI strategies. Overall, the cost-effectiveness performance of single GI was superior to the CGI in pollution control. The single GI strategies were more cost-effective compared to CGI strategies; however it was necessary to invest more to adopt the CGI strategies in order to achieve better pollution control results.