The invention provides a reagent kit for detecting Fumonisin B1 of genetically engineered single-chain antibody and method thereof; in the reagent kit of the invention, the reagent comprises: sample extracting solution, a standard reagent, an enzyme labeled antigen reagent, washing solution, a BSA (bovine serum albumin) regent, a chromogenic substrate and stopping solution; the content of FB1 toxins in the sample is calculated by the following steps of sample processing, regent balancing, washing, adding sampling, washing, color developing and stopping. The Fumonisin B1 single-chain antibody adopted by the reagent kit provided by the invention can be effectively expressed in colon bacillus, and can be produced in a large scale; the producing process is simple, convenient and easy; the time, labor and money are saved. Using the reagent kit in the invention for detecting the Fumonisin B1, whether the sample is polluted by the Fumonisin B1 or not can be determined, and the content of the Fumonisin B1 is calculated in 1.5-2h. The reagent kit is convenient and fast in use, and low in cost.