Abstract:To study the fertilization effects on soil organic carbon, heavy fraction organic carbon, organo-mineral complex status and combined humus in soil and on the yield and quality of Chrysanthemum morifolium, pig manure, chicken manure, rape cake, organic compost and chemical fertilizer were applied in the plot and pot experiments according to the local traditional habit in Sheyang county’s planting base of Chinese medical herbs for two-year planting of Chrysanthemum morifolium. The results indicated: the content of organic carbon in soil decreased with chemical fertilizer which mainly from the loss of light fraction organic carbon. Compared with the treatment without fertilizer, the contents of organic carbon and light fraction organic carbon in soils under different organic manures increased significantly by 4.5% ~ 32.7% and 10.5% ~ 37.8%, respectively. And a 2-year application of organic manures promoted the formation of organo-mineral complex in soils,increased the adding compound and adding complex degree of soils, improved composition of combined humus, increased the content of loosely combined humus, and reduced the content of tightly combined humus, therefore activated soil humus. All kinds of organic manures had a better effect on improving soil fertility under cultivating chrysanthemum morifolium, pig manure the best, then followed by rape cake. Meanwhile, the results of pot experiment showed that all fertilizers increased the biomass of Chrysanthemum morifolium and improved effectively the contents of total flavonoidand and chlorogenic acid of Chrysanthemum morifolium, orgarnic fertilizer having a better effect than chemical fertilizer while rape cake the best, and then followed by pig manure.