Diet composition and feeding habits of the burrowing fish Parapocryptes serperaster were investigated on different fish sizes across dry and wet seasons in the Mekong Delta, Vietnam. The gut length was positively related to fish length; the gut length was 1.57 ± 0.30 times the total length, which is in the range for omnivore (1–3). Detritus, algae and copepods were the main food items in the foregut. The diet composition showed seasonal and intraspecific variations in all fish sizes. The diet diversity varied with fish size and the dry-wet season pattern, and small fish had a higher diet diversity than large fish. The diet evenness index and Costello graphic analysis indicate that this goby is a generalist feeder and feeds mainly on detritus, followed by diatoms, and could obtain food from the bottom and the water column. The feeding intensity of P. serperaster was higher in the wet season than in the dry season, but was not significantly affected by fish size. The P. serperaster fed on Navicula spp. in the wet season, but on Nitzschia spp. in the dry season. The understanding of food and feeding habits of P. serperaster contributes to our knowledge on feeding adaptation of small-bodied bottom dwelling gobies to the mud flat habitats in tropical monsoonal regions.