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Gray mold caused by <i>Botrytis cinerea</i> is a devastating disease in tomatoes. Site-specific fungicide application is still key to disease management; however, chemical control has many drawbacks. Here, the combined application of a biological agent, <i>Clonostachys rosea</i>, with newly developed succinate dehydrogenase inhibitors (SDHI) fungicides showed stronger synergistic effects than the application of SDHI fungicides alone on tomato gray mold control. <i>C. rosea</i> 67-1 has been reported as an efficient biological control agent (BCA) for <i>B. cinerea</i>. Little information is currently available about the combination of <i>C. rosea</i> and fungicides in the control of gray mold. By testing the sensitivity to fungicides with different action mechanisms, <i>C. rosea</i> isolates showed high tolerance to SDHI fungicides (1000 μg mL⁻¹) on PDA, and the conidial germination rate was almost not affected under 120 μg mL⁻¹ of fluxapyroxad and fluopyram. In greenhouse experiments, the control effect of the combination of <i>C. rosea</i> and fluxapyroxad or fluopyram against tomato gray mold was significantly increased than the application of BCA or SDHI fungicides alone, and the combination allows a two-fold reduction of both the fungicide and BCA dose. Further, the biomass of <i>B. cinerea</i> and <i>C. rosea</i> on tomato plants was determined by qPCR. For <i>B. cinerea</i>, the trend of detection level for different treatments was consistent with that of the pot experiments, and the lowest biomass of <i>B. cinerea</i> was found when treated with <i>C. rosea</i> combined with fluxapyroxad and fluopyram, respectively. For <i>C. rosea</i>, qPCR assay confirmed its colonization on tomato plants when mixed with fluopyram and fluxapyroxad. These results indicated that combining <i>C. rosea</i> 67-1 with the SDHI fungicides could synergistically increase control efficacy against tomato gray mold.