Abstract: Different cementing agents were used to prepare three type matrix-based fertilizers. After estimating the slow release capability and the security, matrix-based fertilizer 2 was screened out for tomato production. The biological effects of special matrix-based fertilizer on tomatoes were studied, the results are as follows: when special matrix-based fertilizer for tomato was applied. Root activity of tomato was improved at all growing stages, and the improvement was higher at latter sage. The fruit yield was increased evidently because it is propitious to form yield at latter stage. The ratio of soluble sugar to organic acid, the vitamin C content in tomato fruits were all increased, but the nitrate content in tomato fruits was decreased. At the same time, the utilized efficiency of nitrogen in special matrix-based fertilizer for tomato was enhanced evidently.