Wohushan reservoir is an important drinking water source for south urban area of Jinan, however, the water quality of Wohushan reservoir is not safe, and agricultural non-point source pollution is the main reason that caused the water quality deteriorate. This paper analysed the sources of non-point source pollution through datum of population and agriculture production and other economic and social activities in Wohushan reservoir area. The water quality effect of domestic sewage, house refuse, live stock dung, and unreasonable use of fertilizer and pesticide were discussed as emphasis. Further more, the factors of the non-point source pollution were summarized according to policy, statute, economic, technology etc. At last, countermeasures of non-point source pollution prevention and control were proposed based on the source and pathway control of contaminates including perfect law system, strengthen policy guidance, increase funding, use fertilizer and pesticide reasonably, popularize biotechnology and methane tank, carry out efficient eco-agriculture construction, etc.