Sustainable intensification of protected vegetable crops entails increasing yield while reducing environmental impact and labor input. To explore a comprehensive strategy for high yielding, highly efficient and high quality production of greenhouse tomato (Solanum lycopersicum L.), an integrated crop-nitrogen management (ICNM) strategy was compared to farmers’ traditional management (TM) in a field experiment in a solar greenhouse. A split-plot block design was used. The main factor was the management strategy of ICNM and TM. The secondary factor was four different basal fertilizer treatments, being a control (CK; 0 kg N ha−1), carbon-based urea (BU; 100 kg N ha−1), controlled release urea (CU; 100 kg N ha−1), and conventional compound fertilizer (CF; 100 kg N ha−1). An additional 200 kg N ha−1 through drip irrigation as topdressing was used. Tomato fruit yield, N uptake, and N partial productivity with ICNM were significantly higher than with TM, increasing by 32.1%, 39.7%, and 31.1%, respectively. The proportion of fine roots was increased in ICNM, and the average diameter of roots decreased by 10.7% compared to TM. There was a significant negative correlation between mean root diameter and N uptake. In conclusion, the ICNM strategy was beneficial to form a good root system configuration, promote the development of shoot biological potential, increase tomato yield, maintain fruit quality, increase N uptake, and reduce environmental risks.