Using peanut variety 606 as experimental material, five treatments including CK(no fertilizer application), JCF(applying common compound fertilizer at jointing stage), JCRF(applying controlled-release compound fertilizer at jointing stage), FCF(applying common compound fertilizer at flagging stage), FCRF(applying controlled-release compound fertilizer at flagging stage) were set under the same application rates of N-P2O5-K2O, to test the effects of different fertilizers and different application methods on chlorophyll content, chlorophyll fluorescence parameters of leaves, root system vigor, the nitrate reductase activity and antioxidant activity at different growth stages of peanut. The results showed that there was no significantly difference in Fv/Fm, Fv/Fo and ФPSⅡ between applying controlled-release compound fertilizer and applying common compound fertilizer before pod-setting stage, but the three parameters of applying controlled-release compound fertilizer were significantly higher than those of applying common compound fertilizer at pod-filling and mature stages. Trends of root vigor and nitrate reductase activity were similar with those of Fv/Fm, Fv/Fo and ФPSⅡ. There was no obvious difference in the contents of SOD, POD and APX between applying common compound fertilizer and applying controlled-release compound fertilizer at seedling stage, but these parameters of applying controlled-release compound fertilizer significantly increased at middle and later stage, while MDA content decreased, and topdressing fertilizer at flagging stage was better than that at jointing stage. Controlled-release compound fertilizer had no significant effect on wheat yield, but significantly increased the yield of peanut. The pod yield and kernel yield in the JCRF treatment were increased by 5.1% and 7.6%, respectively, compared with the JCF treatment, and the yields in the FCRF treatment were increased by 5.9% and 8.0%, respectively, compared with the FCF treatment. Under the conditions of same application rates of N-P2O5-K2O and equal nutrient, controlled-release compound fertilizer could meet the nutrient requirement of peanut at the later growth stage, improve the photosynthetic ability of mesophyll cell, enhance root vigor and nitrate reductase activity, and promote nutrient absorption capacity of root system. Meanwhile, controlled-release compound fertilizer could increase the ability of scavenging active oxygen at the late stage, help to delay leaf senescence, thereby improving yield of peanut. Two types of fertilizer both could increase yields of wheat and peanut, and topdressing fertilizer at flagging stage was the best , and the effect of topdressing fertilizer at jointing stage followed.