Fusarium wilt is a soil borne disease caused by plant continuous cropping in monoculture Chrysanthemum morifolium ‘Youxiang’ monoculture not only declines plant quality and yield but also decreases soil enzymes and soil microbial diversity over successive cultivation. In this article, the effects of fungicide (Carbendazim MBC), antifungal enhanced bio-organic fertilizer (BOF), and their combined application on the quality and soil enzymes activities of Chrysanthemum morifolium ‘Youxiang’ in continuous cropping systems were investigated. The results showed that both bioorganic fertilizer (BOF) and fungicide (MBC) single application could effectively prevent the occurrence of Fusarium wilt disease of cut chrysanthemum. Bio-organic fertilizer application was more effective on root activity, soil enzymes activities and quality(shoot height, stem diameter, leaf SPAD value, ray floret number, shoot fresh mass) improvement of cut chrysanthemum, while fungicide single application was responsible for soil enzymatic activities suppression to some extent. The combined application treatment (MBC+BOF) showed the best effects on quality improvement and soil enzyme activities promotion.