With the growing consensus of emerging pollutants and biological toxicity risks in wastewater treatment plant (WWTP) effluents, traditional water quality management based on general chemical parameters no longer meets the new challenges. Here, a first-hand dataset containing 9 conventional parameters, 22 mental and inorganic ions, 25 biotoxicity parameters, and 54 emerging pollutants from effluents of 176 municipal WWTPs across China were measured. Four clustering algorithms and five classification algorithms were applied to 65 well-performing models to determine a novel evaluation parameter system. A total of 14 parameters were selected by semi-supervised machine learning, including TN, TP, NH4+-N, NO2--N, Se, SO42-, Caenorhabditis elegans body width, 72 hpf zebrafish embryo hatching rate, tetracycline, acetaminophen, gemfibrozil, PFBA, PFHxA, and HFPO-DA. These parameters were then used to construct a Healthy Effluent Quality Index model (HEQi). The application efficiency of HEQi was compared with other common methods such as the Water Quality Index (WQI), Fuzzy Synthesized Evaluation (FSE), and Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) in classifying 176 effluents. Results implicated that under the new evaluation criteria, the major task in North and Northeast China remains to reduce the conventional parameters, especially NO2--N. However, it is necessary to strengthen the removal of biotoxicity and emerging pollutants in parts of Central and Eastern China. This study offers new methodological tools and scientific insights for improving water quality assessment and safe discharge of wastewater.