Viruses cause massive bacterial mortality and thus modulate bacteria-governed carbon transfer and nutrient recycling at global scale. The viral shunt hypothesis states the crucial role of viral lysis in retaining microbial carbon into food web processes, while its applicability to nature has not been well identified for over two decades. Here, we conducted nine diel surveys in the tropical South China Sea and suggested that the time scale adopted in sampling and system trophic status determine the "visibility" of the viral shunt in the field. Specifically, viral abundance (VA), bacterial biomass (BB), and bacterial specific growth rate (SGR) varied synchronously and presented the significant VA-BB and VA-SGR linkages at an hourly scale, which reveals direct interactions between viruses and their hosts. The differential responses of the viral shunt to temperature, i.e., looser VA-SGR coupling in warm and tighter VA-SGR coupling in cold environments, imply an altered carbon cycling in tropical oceans under climatic warming.