Abstract: [Objective] To make clear the effects of several different formula of cattle dung,sheep dung,changes in microflora of chicken manure organic fertilizer fermentation process and their effects on seedling.[Method] Different formulas were used to treat cattle,sheep,chicken manure,respectively and after 30 days of insulation,anaerobic fermentation was used to produce organic fertilizer,and PCR-DGGE,BIOLOG technology was applied to analyze the change of microbial community and the activity of carbon metabolism.Finally tomato hole tray seedling experiments were conducted to evaluate the fertilizers efficiency.[Result] Bacterial manure microorganisms isolated from DGGE were lactic acid bacteria (Lactobacillus sp.) and Wei Sishi bacteria genera (Weissella sp.) which accounted for a larger proportion.Lactic acid bacteria (Lactobacillus sp.)was 40.4; Weiss's species (Weissella sp.) was 23.8;.As could be seen from the average color rate (AWCD) Shannon-Wiener index (H') sheep droppings were higher than the levels of chicken manure and cattle dung.Principal component analysis showed that there were differences in the utilization of carbon source in the 3 treatment groups.There were differences between YⅢ and YⅣ treatments.The community structure of JⅡ and JⅢ in chicken manure treatment group was relatively consistent and there were differences between JⅠ and JⅣ.Seedling test results showed that the different treatments had different effects on the 4 indexes of plants,and there was a great difference.[Conclusion] Different formulae for treating cattle,sheep,chicken manure fertilizer flora structure have a significant impact.Tomato seedling experiments show that N3,Y3 and J1 processing have the best fertilizer effect.The average plant height of tomato seedlings is 25.5; and 26.16;,higher than that of CK.