The microbial metabolic state of the oligotrophic ocean, the largest biome on Earth, has an important impact on the efficiency of biological pump and the marine carbon cycle. Measurements of microbial metabolism in the euphotic zone (0–200m) and mesopelagic zone (200–1,000 m) along the western Pacific boundary during December 2021 and January 2022 were made using in vitro incubations. Microbial community respiration (MCR) in the summed and in each of the 0.2–0.8 μm (Bacterial respiration, BR) and >0.8 μm size-fractions in the euphotic zone were higher than in the mesopelagic zone. So it is with bacterial production (BP) as well. Total depth-integrated microbial metabolism in the mesopelagic zone was higher than in the euphotic zone, except BR. Compared with cell-specific BP which decreased with depth, cell-specific BR was significantly higher in the mesopelagic zone. With the proportion of BR in CR increased, BR was dominant in the mesopelagic zone. There was a significant negative correlation between euphotic nutrient concentration and microbial metabolism. Chlorophyll a (Chl a) was of great importance in affecting microbial metabolism. The attenuation rate of POC in the mesopelagic zone in the western Pacific was comparable to that of the ALOHA station, which was higher than that of other regions. Overall, our results revealed that output productivity in the euphotic zone had an important impact on the underlying water and that microorganisms in the mesopelagic zone in low-latitude oligotrophic waters had active bioactivity and high POC mineralization rates.