The determination of the total amount of water pollutant emission in different regions is a difficult problem faced by managers and researchers. Previous studies mostly focused on operability and fairness with little attention paid to local water quality. In order to make total emission pollutant control (TEPC) truly serve the improvement of water quality, a water total emission pollutant allocation model was built based on water environmental carrying capacity (WECC) in this paper. This model was used to construct a water pollutant emission control allocation scheme for 28 cities in Henan Province, China. The results showed that the chemical oxygen demand (COD) reduction rates for these cities ranged from 16.8 to 38.6% and ammonia-nitrogen (NH3-N) reduction rates ranged from 5.7 to 43.5% in 2020, which were different from the previous targets for these cities without considering their current status of water quality. The largest COD reduction rates for different types of point sources (industrial, urban, and large-scale livestock sources) were 35.4%, 39.0%, and 38.0%, respectively, and the largest NH3-N reduction rates were 62.2%, 42.5%, and 43.5%, respectively. This study solves the problem of long-term disconnection between TEPC and water quality improvement in China. The results can also be applied to implement the TEPC to improve water quality in other regions with a similar problem.