Excessive application of chemical fertilizers is the primary source of nitrogen (N) and phosphorus (P) losses from planting industries in the Guangdong-Hong Kong-Macao Greater Bay Area. Establishing fertilization model that combined optimized fertilizer input with organic fertilizer is a key technological approach to improve partial factor productivity of nitrogen and phosphorus fertilizer and mitigate non-point source pollution in vegetable planting field in this location. Therefore, a field experiment was conducted with three treatments: conventional fertilizer management (CM), 30% N input reduction with 20% organic fertilizer N replacement (RP), and RP combined with slow-release compound fertilizer (CRFP). The results showed that, compared with CM, CRFP treatments increased vegetable yield by 12.4%, yield N and P uptake by 15.8% and 15.6%, respectively, while reduced runoff N and P losses by 46.7% and 56.8%. In terms of cost and reward, the total cost under CRFP treatments was 43,600 yuan·hm-2, which was 12.4% lower than that under CM, while the net economic benefit was improved by 48.8%. Integrating environmental and economic indicators, the strategy of 30% N input reduction combined with 20% pig manure N replacement and slow-release compound fertilizer (CRFP) application could simultaneously enhance vegetable yield and reduce surface runoff N and P losses by rainfall events. This approach is suitable for promotion and application in vegetable cultivation within the Guangdong–Hong Kong–Macao Greater Bay Area.