Abstract:[Background] Endophytic fungi is a reservoir of bioactive small-molecular natural compounds, but it is difficult to obtain structurally novel compounds and pronouncedly active analogues because of enormous species dispersed in nature, and repeated isolation became an bottleneck in the mining process. [Objective] The objective is to rapidly find new biologically active metabolites with combination of LC-MS, DNP and bioactivity evaluation. [Methods] Pure metabolite was isolated through silica gel and recrystallization. The structure was elucidated by spectroscopic and X-Ray techniques. The biological activity was evaluated through 96-well dilution method. [Results] Eleven endophytes were isolated and identified from B. balsamifera (L.) DC. A targeted endophyte identified as Diaporthe sp. was selected and an active compound Cytochalasin H was afforded from the rice extract of this fungus, its inhibitory effects against Bacillus subtilis was assayed with a MIC value of 32 μg/mL. [Conclusion] This study introduced a new extensive method in mining for bioactive secondary metabolites from endophytes of B. balsamifera (L.) DC., which provides references for rapidly exploration of effective lead agents.