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Sorting nexins are a conserved protein family involved in many cellular processes in fungi, and the function of sorting nexin Snx4 (Atg24) and Snx41 (Atg20) in <i>Cochliobolus heterostrophus</i> was not clear. The Δ<i>Chsnx4</i> and Δ<i>Chsnx41</i> mutants were generated by a PCR-based marker method to determine the roles of Snx4 and Snx41 in reproductive development, stress adaption, and virulence in <i>C. heterostrophus</i>. Compared with the wild-type strain, the Δ<i>Chsnx4</i> and Δ<i>Chsnx41</i> mutants exhibited obvious changes in vegetative growth and in morphology of conidia. In addition, the conidiation, appressorium formation, and virulence of snx4 and snx41 mutants were dramatically reduced. Moreover, Δ<i>Chsnx4</i> and Δ<i>Chsnx41</i> mutants were more sensitive to oxidative stress (menadione and H₂O₂), cell wall integrity stress (Congo red and calcofluor white), fungicides, and isothiocyanates. All the phenotypes mentioned above were restored in complemented strains. In addition, ChSnx4 and ChSnx41 were proven to interact with each other through yeast two-hybrid. Taken together, these findings indicated that <i>ChSNX4</i> and <i>ChSNX41</i> were important for fungal growth, asexual development, stress adaption, and virulence in <i>C. heterostrophus</i>.