In order to study species and distribution of the endophytic fungi in overwinter jujube, and screen anti-microorganism endophytic fungi for controlling jujube fruit shrink disease, 225 strains of endophytic fungi were obtained from bark, stem and wattle in overwinter healthy jujube, 12 genera were identified, and Phoma, Alternaria, Chaetomium and Fusarium were dominant genera. The results showed that endophytic fungi distributed in different tissues of overwinter healthy jujube, and species were abundant. Species and quantity of endophytic fungi were different in different tissues from different varieties. The results of indoor plate confrontation test showed that 25 strains showed inhibitive activity against Phoma 1-2 in the 225 strains tested, and the highest inhibitive rate was 85.45%; 14 strains showed inhibitive activity against Fusicoccum 1-5, and the highest inhibitive rate was 76.00%. The stains F7 and F8 showed strong inhibitive activities against the two pathogens, and had clear inhibitive zone. It showed that the two stains could provide antimicrobial metabolites.