In recent years, the quality and security of vegetables have being increasingly concerned by people and investigated by researchers. However, vegetable quality decline is very common due to excessive irrigation and irrational fertilization. The nitrate content is an important index which is used to evaluate vegetable quality. Although tomatoes have been grown successfully for many years in many parts of the world, there is no accurate formula or recipe on both the amount of irrigation and fertilizer levels to get high quality tomato fruit. Alternate partial root-zone irrigation (APRI) is a new water-saving technique and may improve crop water use efficiency and fertilizer use efficiency. To determine the effects of irrigation amount and fertilizer rates of nitrogen, phosphorus, potassium and manure on the nitrate content in tomato fruits under APRI, the quadratic orthogonal regressive rotation design with five factors was used in pot experiment, in which five rates were set for every experimental factor. A regression model on the amount of irrigation water and fertilizers and the nitrate content in tomato fruits was established. Based on the regression equation, the single, interactive and coupling effects of these five experimental factors on the nitrate content in tomato fruit were analyzed. The results showed that if other factors were zero codes, the nitrate content in tomato decreased firstly and then rose with irrigation water increase, while it showed a reverse trend with N and P fertilizer levels. The nitrate content in tomato increased gradually with manure amount, but it was not affected by K fertilizer level. The interactions on the nitrate content in tomato fruits between P fertilizer and manure levels, N and P fertilizer levels showed positive effects, while the interactions between irrigation amount and K fertilizer or manure level, as well as N and K fertilizer levels were negative effects. The coupling effects between two of these five experimental factors showed that the nitrate content in tomato fruits increased markedly with higher irrigation amount when no manure was applied, while it decreased firstly and then increased with irrigation amount for the other manure and all K fertilizer rates. The nitrate content in tomato decreased with K fertilizer or manure increase when irrigation amount was above the mid level. The nitrate content in tomato increased firstly and then decreased with N fertilizer increase for any P or K fertilizer rate. The nitrate content was less when P fertilizer rate was at the highest than any other level,and it was the lowest when P and N fertilizer rate were at the highest and the lowest, respectively, suggesting that lower N fertilizer and higher P fertilizer rates could decrease the accumulation of nitrate content in tomatoes. Interestingly, the situation was different for K fertilizer. Higher K fertilizer rate could reduce the nitrate content significantly only when the N fertilizer rate was above the mid level. The coupling effects of P fertilizer with manure rates on the nitrate content in tomato fruits indicated that increasing P fertilizer properly and decreasing manure application at the same time could greatly contribute to less nitrate content in tomato fruits.