Isoprothiolane (IPT) resistance has emerged inMagnaporthe oryzae, due to the long-term usage of IPT to control rice blast in China, yet the mechanisms of the resistance remain largely unknown. Through IPT adaptation on PDA medium, we obtained a variety of IPT-resistant mutants. Based on their EC50values to IPT, the resistant mutants were mainly divided into three distinct categories, i.e., low resistance (LR, 6.5 ≤ EC50< 13.0 μg/mL), moderate resistance 1 (MR-1, 13.0 ≤ EC50< 25.0 μg/mL), and moderate resistance 2 (MR-2, 25.0 ≤ EC50< 35.0 μg/mL). Molecular analysis ofMoIRR(Magnaporthe oryzaeisoprothiolane resistance related) gene demonstrated that it was associated only with the moderate resistance in MR-2 mutants, indicating that other mechanisms were associated with resistance in LR and MR-1 mutants. In this study, we mainly focused on the characterization of low resistance to IPT inM.oryzae. Mycelial growth and conidial germination were significantly reduced, indicating fitness penalties in LR mutants. Based on the differences of whole genome sequences between parental isolate and LR mutants, we identified a conservedMoVelBgene, encoding the velvet family transcription factor, and genetic transformation of wild type isolate verified thatMoVelBgene was associated with the low resistance. Based on molecular analysis, we further demonstrated that the velvet family proteins VelB and VeA were indispensable for IPT toxicity and the deformation of the VelB-VeA-LaeA complex played a vital role for the low IPT-resistance inM.oryzae, most likely through the down-regulation of the secondary metabolism-related genes or CYP450 genes to reduce the toxicity of IPT.