The invention provides a probe set and a reagent kit used for detecting pathopoiesia/susceptibility genes of congenital megacolon and relative syndromes. At most 172 pathopoiesia/susceptibility genes related to diseases can be detected at the same time, and reference can be provided for affected individual molecular genetics diagnosis, mass survey of congenital megacolon high-incidence areas, screening of high-risk affected groups in congenital megacolon family members and corresponding genetic counseling or prenatal intervention.