The invention discloses a strain of euonymus japonicus endophytic bacterium bacillus methylotrophicus HYEB 5-6 which was preserved in China Center for Type Culture Collection on Dec 8th, 2015, and the preservation serial number is CCTCC No: M2015728. The bacillus methylotrophicus HYEB 5-6 is an euonymus japonicus endophytic bacterium and can delay germination of euonymus japonicus anthrax conidium, inhibit extension of a germ tube, inhibit germination of the conidium, induce hypha to generate an expanded body and cause malformation of the hypha; it is proved by inoculation experiment results that after HYEB 5-6 thallus is sprayed, the index of decease infection of euonymus japonicus anthracnose is remarkably inhibited, and scabs of euonymus japonicus anthracnose are reduced; the HYEB 5-6 strain has a certain antagonistic effect on euonymus japonicus colletotrichum, alternaria spp, cytospora chrysosperma, higgins dish bacteria, magnaporthe oryzae, rhizoctonia, horse chestnut fusicoccin and fusarium solani.