The invention relates to microbe technology, in particular to a degrading enzyme preparation for degrading residual organic phosphorus on vegetables and fruits and a preparation method thereof. The invention particularly relates to organic phosphorus degrading enzyme preparation obtained by fermenting Methylobacterium. The preparation process comprises the following steps: after fermenting the inoculated strain, centrifugally collecting thalli, and breaking thalli to obtain the organic phosphorus degrading enzyme preparation. The organic phosphorus pesticide degrading enzyme preparation can degrade residual organic phosphorus pesticides on vegetables and fruits.