Biogas slurry, a liquid organic fertilizer, has been idely used in agricultural production. However, the characteristics of high water content and low fertility make it always applied empirically and a scientific and reasonable application of biogas slurry is urgent needed in practical agricultural production. This study aims to explore the effects of various biogas slurry concentrations on the yield, comprehensive nutritional quality (CNQ), irrigation water use efficiency (IWUE) and partial factor productivity of nitrogen (PFPN) of tomatoes in a greenhouse. Seven treatments, including Ti (BS1:4; 0.8Ep), T2 (BS1:6; 0.8Ep), and T3(BS1:8; 0.8Ep), T4(BS1:4; 0.6Ep), T5(BS1:4; 1.0Ep), CK (no fertilization; 1.0Ep), CF (conventional chemical fertilization; 1.0Ep) were set up, where BS1:4, BS1:6, and BS1:8 are the volume ratio of biogas slurry to water, 0.6, 0.8, and 1.0 were crop dish coefficients, respectively. Ep is the evaporation amount of a 20 cm standard evaporating dish. The results showed that appropriate application of biogas slurry had a positive impact on crop growth such as total dry biomass, plant height, stem diameter and finally increased the yields, in which Ti treatment was the best. The fruit yield increased with the increase of biogas slurry ratio for treatments at the same irrigation level of 0.8Ep and the maximum yield of single tomato can reach 5.174 kg. The IWUE increased with the decrease of irrigation for treatments at the same biogas slurry ratio of BS1:4 and T4 treatment had the highest IWUE. The CNQ first increased and then decreased with the increase of biogas slurry ratio under the same irrigation level of 0.8Ep and T2 treatment obtained the highest CNQ; but the PFPN decreased with the increase of biogas slurry ratio and T3 treatment acquired the largest PFPN. Within an 80% confidence interval, when the irrigation amount was in a range of 39.233 similar to 43.134 L and the nitrogen quantities was 7.983 similar to 8.426g, the yield, IWUE, CNQ, and PFPN can reach >= 80% of their maximums at the same time. Taking into account the growth, yield, fruit quality, and water and fertilizer use efficiency, T1 treatment was the best fertigation strategy for a higher production and better quality. The results can provide some help for scientific management of biogas slurry application in greenhouse.