Excessive water and fertilizer inputs have led to a series of environmental problems in vegetable production areas in China. Identifying the fates of water and nutrients is crucial to develop best management strategies in intensive vegetable production systems. The objectives of this study were to (i) develop a scientific water and nitrogen (N) management tool for intensive greenhouse vegetable production in China, and (ii) evaluate the model performance in the simulating the fate of water and N, and vegetable growth under different water and N management practices in China. A vegetable growth component was added to the field soil-crop system model WHCNS (soil Water Heat Carbon Nitrogen Simulator), named WHCNS_Veg. Parameters for the model were estimated and a sensitivity analysis was conducted by coupling the model with the model-independent parameter estimation program (PEST). Data used to test the model came from two years of cucumber and tomato experiments with various water and N combinations in Shandong province, China. The results of sensitivity analysis showed that the soil hydraulic parameters and vegetable genetic parameters had a relatively higher sensitivity compared with those of N transformation parameters. The saturated soil water content had the highest sensitivity among soil hydraulic parameters, and the total available accumulated temperature, crop coefficient and maximum root depth had higher sensitivity for both vegetable crops. Among the N transformation parameters, the parameters related to nitrification had the highest sensitivity. The automatic optimization algorithm performed well in adjusting soil hydraulic parameters, vegetable genetic parameters and N transformation parameters. The normalized root mean square error for soil water content, soil nitrate concentration, marketable fresh yield and vegetable N uptake were 5.7%, 28.0%, 2.7% and 8.3%, respectively, and indices of agreement were 0.727, 0.730, 0.997 and 0.832, respectively. The results indicated that the WHCNS_Veg model has great potential to simulate and analyze water and N fates, and vegetable growth for the intensive greenhouse vegetable production in China.