The urban river eco-health is an important concern for researchers and scholars. To comprehensively evaluate the eco-health status of city river in the mesothermal zone, we used the Yitong River, which is one of the major representative rivers of the cities in northern China, as an example; the monitoring and analysis of water environmental factors, plankton, and heavy metal elements within its watershed were conducted in the autumn and winter of 2022. Based on a single-factor assessment of the health status of the Yitong River, a TOPSIS model was constructed to assess the eco-health status of the river by objectively allocating weights to each indicator. The research showed that most of the sampling sites were rated as "moderate" based on the Water Quality Index (WQI) method. The results of the evaluation on the basis of the Planktonic Index of Biotic Integrity (P-IBI) method showed that the proportion of stations with a rating greater than "moderate," in autumn and winter seasons of the Yitong River, was 50% and 30%, respectively. The Absolute Principal Component Score-Multiple Linear Regression (APCS-MLR) model was used to analyze the physical origins of metals in the river. The results showed that the sources of pollution in the Yitong River in autumn could be divided into natural, industrial, and agricultural sources, while in winter, they were attributed to agriculture, transportation, industry, and atmospheric deposition sources. The assessment of potential risks from heavy metals showed that the results were similar for the evaluation sites in autumn, while the potential risk was more severe in the urban reaches than in the rural reaches in winter. The results of the comprehensive ecological risk health assessment of the Yitong River on the basis of the improved TOPSIS model showed that the health position of the Yitong River was "Low" in autumn and winter, with a decreasing trend from the upstream to the downstream in autumn, and that the urban section of the river was more polluted than the rural section in winter. The results of related analyses proved that heavy metals are the main factor limiting the comprehensive eco-health of the Yitong River. Therefore, controlling the sinking of heavy metals into the Yitong River basin may be an effective way to maintain its eco-health.