In the present study, the diversity, tissue distribution, and biocontrol potential of cultivable endophytic fungi harbored in P. notoginseng plants were described for the first time. We proposed that the endophytic fungi would exert certain functions to help the host survive in plantation against disastrous root-rot diseases. In the survived and healthy notoginseng plants, the harbored fungal endophytes may give some clue to find effective approaches to control root rot, caused by complex pathogens. Thus, in order to screen for the most promising endophytes, we evaluated the potential of all the endophytic isolates as BCAs by challenging five major root-rot pathogens of the host plant, A. panax, F. oxysporum, F. solani, Phoma herbarum, and M. acerina, whose pathogenicity was confirmed in our previous work. Among the isolates, crude extracts of PH30409 and PH30441 showed strong inhibition on all tested phytopathogens, implicating that the two isolates have the potential to produce active compounds.