Rice blast (Magnaporthe grisea) and sheath blight (Rhizoctonia solani) are limiting factors for rice production. Co-infection of these pathogens results in a disease complex which is difficult to control. In China, growers are accustomed to applying individual fungicides to manage blast and sheath blight, which require large amounts of labor. Application to seedling trays is a new promising solution for saving labor. In this study, application of combined fungicides with different modes of action to seedling trays to integrate control rice blast and sheath blight was evaluated in vitro assays and field trials. The results showed that the combination of thifluzamide and tricyclazole in the 1:2 ratio had significant synergistic inhibitory effects on the mycelial growth of M. grisea and R. solani, with a synergistic ratio (SR) of 2.17 and 1.49. Results from field trials revealed that thifluzamide + tricyclazole at 1107 and 958.5 g/ha applied to seedling trays was the most effective treatment to reduce the disease index of rice blast with control effects of 83.74–84.96% and 81.34–83.26% in 2022 and 2023, respectively, and no significant differences were observed from tricyclazole at 300 g/ha as foliar sprays twice. Compared to the untreated control, disease index of rice sheath blight was notably reduced by all treatments containing thifluzamide. The highest control was recorded in the treatment of thifluzamide + tricyclazole applied at 1107 g/ha to seedling trays. Moreover, compared to the untreated control, all treatments significantly enhanced rice grain yield by 7.67–17.86% and 3.38–18.91% in 2022 and 2023, respectively. The greatest yield (7429.73 and 7404.73 kg/ha in 2022 and 2023, respectively) was observed from the treatment of thifluzamide + tricyclazole at 1107 g/ha applied to seedling trays, with no significant differences among all the treatments containing tricyclazole. Taken together, these results indicated that seedling tray application of thifluzamide + tricyclazole could be a labor-saving approach to the integrated control of rice blast and sheath blight disease complex, while increasing rice grain yield.