In coral reefs, heterotrophic bacteria play an important role in driving carbon cycle and sustaining coral health. Bacterial production (BP), bacterial respiration (BR) and bacterial community composition (BCC) were determined in the Luhuitou fringing reef and the surrounding ocean in the northern South China Sea on a seasonal basis, in order to examine bacterial metabolic activity and effect of temperature on bacterial community in the fringing coral reef. Our results showed that higher BP (3.52–12.45 μg C L d) and bacterial growth efficiency (0.16–0.28) and lower cellular BR (8.34–31.73 fg C cell d) in the Luhuitou fringing reef than the surrounding ocean was more likely attributed to substrate availability. Enhanced dissolved organic nitrogen availability preferentially triggered the growth of bacteria with high nucleic acid content (HNA bacteria), which was most possibly responsible for high BP in the coral reef. Heterotrophic bacteria were more sensitive to temperature in the highly productive Luhuitou fringing reef than the surrounding ocean. Temperature shaped BCC by mediating enzymatic activity in the coral reef, likely triggering opportunistic infections. Warming might not only promote the growth of HNA bacteria and shift BCC in the coral reef, which was partly responsible for coral disease, but also reduce oxygen replenishment from the surface due to stratification and elevate the oxygen consumption owing to high BR, consequently threatening the survival of corals. Our findings helped to better understand how heterotrophic bacteria mediated the survival of corals in response to fluctuations of temperature.