Effective microorganism (EM) technique is a preferable means on wastes treatment, and could promote to stimulate plant growth and soil fertility in agriculture. In this study, EM stoste was enriched by adding molasses and distilled water, and the wastewaters were treated with different EM stoste treatments and EM enrichment treatments, then the EM-treated wastewaters were used for the irrigation of tomatoes. The indexes including vitamin C, soluble protein, soluble sugar and nitrate were used to evaluate the tomato quality, and projection pursuit model was introduced to select the optimal scheme for wastewater treatments. Results showed that: (1) T3 was supposed to be the recommended enrichment scheme, proportion of which was 6% EM stoste, 6% molasses and 88% distilled water, (2) EM enrichment solution had more significant effects in decreasing the COD_Cr value of wastewaters since which enhanced harmony and adaptation of microorganisms, and S1 (600ml wastewater, 200ml activated sludge, 10ml EM enrichment solution, and under aeration condition) was preferable for the degradation of COD_Cr in wastewaters, (3) Dynamics of tomato plant height with different EM-treated wastewater treatments could be well presented by the exponential models, and R² reached a considerably high value of 0.9707- 0.9909, (4) According to the analysis of Vitamin C, soluble protein, soluble sugar and nitrate in tomato fruits with different schemes, S1 and S2 scheme appeared to obtain the tomatoes with better quality, (5) S1 was recommended as the optimal scheme based on the analysis of comprehensive indexes, indicating a preferable result in not only the treatment of wastewaters but also the cultivation of tomatoes. The study conclusions could provide practical basis for biological processing techniques of wastewater and the reutilization of wastewater in agricultural production.