Heterotrophic bacteria play a vital role in the marine carbon cycle and viruses are an important regulator of bacterial metabolism and community composition. It remains unclear about how bacteria-virus interactions vary with environmental conditions in oceans. In this study, bacterial metabolic activity and community composition were examined in three treatments with different viral pressure (control, virus-rich and virus-reduced) through bioassay experiments at three stations with different environmental conditions in the shelf of the northern South China Sea. Our results showed that bacteria-virus interactions varied with environmental conditions. Viral lysis mediated bacterial growth rate (BGR) and production by shaping bacterial community composition. Furthermore, the effect of viral lysis on bacterial growth rate and production was reduced in substrate-rich waters compared to substrate-low waters. However, the opposite pattern occurred for viral regulation on bacterial respiration and carbon demand, likely since viral lysis dramatically mitigated the maintenance respiration of bacteria. Consequently, viral lysis to greater extent mitigated bacterial carbon processing in substrate-rich environments than in substrate-low environments. Our findings provided new insights into bacteria-virus interactions, and improved our understanding of the role microbial processes in carbon cycling in oceans.