Sheath blight, causes by Rhizoctonia spp., threaten maize yield every year throughout the world. Trichoderma could degrade Rhizoctonia solani on maize mainly via competition and hyperparasitism, whereas validamycin A could efficiently inhibit the growth of R. solani via disturbing the energy system. By contrast, validamycin A is efficient but it takes effect in a short period, while Trichoderma takes effect in a long period though time-consuming. To overcome the disadvantages, Trichoderma asperellum GDFS1009 was used together with validamycin A. In vitro tests proved that the combined pathogen-inhibiting efficiency was significantly improved. Furthermore, results based on transcriptome and metabolome showed that validamycin A had no significant effects on growth, basic metabolism and main bio-control mechanisms of T. asperellum GDFS1009. Such few impacts may be attributed to detoxification and tolerance mechanism of T. asperellum GDFS1009. In addition, T. asperellum GDFS1009 has an ability to relieve the stress caused by validaymicn A. Meanwhile, liquid chromatography-mass spectrometry (LC-MS) results showed that only minor degradation (20%) of validamycin A was caused by T. asperellum GDFS1009 during cofermentation. All results together provide solid bases for validamycin A synergy with T. asperellum GDFS1009 in their combined biocontrol application.