Rice is an important agricultural crop in Vietnam. Nematodes are diverse in soil agroecosystems. However, little is known about their seasonal variation in extremely intensive rice cultivation in tropical regions. The objectives of this study were to investigate the seasonal variation and spatial distribution of the nematode community, and to assess its relationship with the soil chemical property and rice yield. Soils (0-10 cm and 10-20 cm deep) were collected at harvest in spring-summer (S-S), summer-autumn (S-A), and winter-spring (W-S) cultivation in 2017 and 2018. Plant-parasitic nematodes were the largest group and accounted for 47-80 and 79-92% of total nematode abundance in the topsoil and subsoil, respectively. Hirschmanniella was the most dominant taxon whose abundance in topsoil varied from 275-739 in W-S to 1010-1270 indiv. (100 g soil)−1 in the S-S season. Nematode assemblages differed between topsoil and subsoil, and those of topsoil had clear seasonal distribution patterns. Bacterivore nematodes were the predominant group of free-living nematodes, with increasing relative abundance in the topsoil of S-S (average 23.2% of total free-living nematodes) < S-A (average 41.9%) < W-S (average 57.3%). Furthermore, soil in the W-S season had the highest microbial activity in 2018. Soil pH, EC and abundance of Hirschmanniella spp. were significantly negatively related with rice yield. The present results suggest that the presence of Hirschmanniella spp. in soil may be involved in a reduction of rice yield in the triple rice system.