To select suitable slow-release fertilizers for sugarcane productions the endophytic bacterial community structure in the stems of sugarcane under different slow-release fertilizer applications were analyzed. Based on high-throughput sequencing techniques, the endophytic bacterial community structure in the stems of sugarcanes among conventional fertilization (CK) and different slow-release fertilizers (A-F treatments) were analyzed. In comparison with CK, the diversity of the endophytic bacteria in the stems of sugarcanes was significantly increased by adding long- acting agent (235 g/t) and synergist (3 g/t and 18 g/t), but the richness of the endophytic bacteria in the stems of sugarcanes was not significantly improved by slow-release fertilizer applications except adding long-acting agent (235 g/t) treatment C. Meanwhile, Herbaspirillum was the specific endophytic dominant bacterial genus in CK. Sporocytophaga and Cellvibrio were the unique endophytic dominant bacterial genera in the slow-release fertilizer adding long-acting agent (125 g/t) treatment A. However, no specific endophytic dominant bacterial genera could be found in the slow-release fertilizer adding long-acting agent (150 g/t) treatment B. Norank_f__SC-I-84, norank_f__Neisseriaceae, norank_f__JG30-KF-AS9 and Massilia were the specific endophytic dominant bacterial genera in the slow-release fertilizer adding long-acting agent (235 g/t) treatment C. Brevundimonas, Enterobacter, Staphylococcus were the unique endophytic dominant bacterial genera in the slow-release fertilizer adding synergist (3 g/t) treatment D. Cloacibacterium was the specific endophytic dominant bacterial genus in the slow-release fertilizer adding synergist (8 g/t) treatment E. And unclassified_f__Burkholderiaceae, Paenibacillus, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Corynebacterium_1, Chryseobacterium were the specific endophytic dominant bacterial genera in the slow-release fertilizer of adding synergist (18 g/t) treatment F. Furthermore, the functions of the endophytic bacteria in the stems of sugarcanes did not show significantly different between CK and applications of slow-release fertilizer treatments. In comparison with CK, the diversity of the endophytic bacteria in the stems of sugarcanes was significantly increased by adding longacting agent (235 g/t) and synergist (3 g/t and 18 g/t), but the richness only could be significantly improved by application with slow-release fertilizer adding with long-acting agent (235 g/t) treatment C. Except of slow-release fertilizers +long-term agent (150 g/t) treatment B, specific endophytic bacterial genera in the stems of sugarcanes all could be detected under slow-release fertilizer applications. Although the whole functions of the endophytic bacteria in the stems of sugarcanes were not significantly altered by slow-release fertilizer applications, higher stress resistant abilities could be concluded in sugarcanes under most of slow-release fertilizer applications (B-F treatments). Among them, the highest promotion and stress resistant effect on sugarcanes growth was the slow-release fertilizer + 235 g/t long-acting agent treatment (C) according to the composition and function of endophytic bacteria in stems of sugarcanes.