The invention relates to an ecological activity deodorant and a preparation method thereof. The ecological activity deodorant contains bacillus subtilis XJ3 with a preservation number of CGMCC No.12746 and candida mycoderma bacteria JM1 with the preservation number of CGMCC No.12747, which are preserved in China General Microbiological Culture Collection Center (CGMCC for short), and the preservation time is July, 8th, 2016. The invention also comprises the preparation method of the ecological activity deodorant. The ecological activity deodorant has obvious deodorizing effect, cowhouse bacteriostasis effect is obvious, at the same time, ammonia gas and hydrogen sulfide release amount is reduced.