The effects of different N rates on nitrate nitrogen accumulation of soil, soil conductivity, pH and the production and quality of vegetables were studied by the field plot experiment at different fertilizer levels in greenhouse of Taihu Lake region. The results showed that nitrate nitrogen accumulation of soil was proportional with the N rates, and the nitrate nitrogen content of soil reached to 221.35 mg/kg from 35 mg/kg after two seasons of vegetable cultivation under the farmer’s habitual N usage. Soil conductivity and pH were significantly correlated with nitrate nitrogen content, and soil conductivity was more obvious (the correlation coefficient was 0.832). The results also showed that nitrate nitrogen accumulation caused the declines in production and quality of vegetables, for example, compared with N3 experiment (lettuce season: N 312 kg/hm2; celery season: N 384 kg/hm2), the productions of lettuce and celery were reduced by 11.8% and 33.9% respectively under farmer’s habitual N usage, meanwhile vitamin C contents were reduced by 17% and 36.6% while nitrate contents increased 22.3% and 32%, respectively. Nitrate contents of vegetables increased to the 3rd pollution level under farmer’s habitual N usage and it would be harmful to human health.