Forest is titled as “green reservoir” which has incredible ecological functions, such as: reserving water, depurating water quality, etc. Therefore, understanding the effects of different components of the forest ecosystem on water quality is significant. In this study, the Picea schrenkiana var.tianschanica natural forest was taken as the object in the middle Tianshan mountains at Tianshan Forest Ecosystem Research Station. There are totally eight sample plots according to the forest canopy density (0.2, 0.4, 0.6, and 0.8) and forest age (young forest (0-60a), middle\\aged forest (60-100a), nearly mature forest (100-120a), and mature forest (120-160a)) in this area. In the plant growing season (July, August, September), all of water samples in the condition of rainfall over 30mm were collected using high-density polyethylene plastic bottle and detected in Xinjiang Environmental Monitoring Station. The water quality changes during rainfall transformation process were investigated on rain fall, through fall, surface runoff and underground seepage water. The water samples were analyzed chemically to determine the effects of different ecosystem components on water quality. The results showed that: (1) The influence of forest ecosystem on water quality of rainfall was enhanced as the canopy density and forest age increased. When forests were in same age, the sequence of this influence on water quality was canopy density of 0.2＜0.4＜0.6＜0.8. When canopy density was 0.8, the sequence of forest influence on water quality was young forest＜middle-aged forest＜mature forest＜near mature forest; (2)When the rainfall entered forest canopy, the nutrient content in water was significantly increased as dissolved oxygen decreased and ammonia nitrogen, COD, BOD, total phosphorus as well as potassium content increased; (3) When the through fall turned into surface runoff, the concentration of dissolved oxygen in water further declined, along with COD, BOD, total phosphorus and potassium content increased. Meanwhile, the ammonia nitrogen concentration remarkably decreased; (4) The soil layer had strong decontaminating ability and high nutrient accumulation function in natural forest ecosystem. The water quality indicator of total underground seepage was much better than those of precipitation, indicating that forest soil layer is the most critical layer of the forest ecosystem. (5) The sequence of the water quality in the forest ecosystem scored by quantitative and comprehensive assessment on was July＞September＞August; (6) The multi-factor line model established by principal component analysis (PAC) method was representative and can be better used for comprehensive assessment on water quality.