The pollution in Henan reaches of Shayinghe River is the most serious section in the Huaihe River and is also the most important government of water pollution control project. This article selected the Jieshou cross section which could reflected the pollution situation in Henan reaches of Shayinghe River as the represent cross section, analyzed the annual changes of water quality and influence factors by qualitative. Through the analysis, it turned out that the NH3-N and CODMn (the potassium permanganate index) is the major effect indexes for water quality, and the water quality change is close with the wheat growing period, rainfall, the rain flood distribution et.al. So we must develop the ecological agriculture, enhance the scientific level of gate operation so as to deal with the surface source contamination concerning with the rainstorm.