Long-term intensive rice monoculture, triple rice cultivation (rice crops are cultivated three times per year) in the Mekong Delta, Vietnam, causes a reduction in topsoil quality. Rotating rice with an upland crop in a tropical paddy field may improve the soil physicochemical properties but effects on the soil nematode community are unknown. This study was conducted in a triple rice field to evaluate the responses of the nematode community to a crop rotation (the first rice in a year was replaced with sesame and soybean, and the second and third crops were rice) and to organic amendment. The experiment was based on a split-plot design with two factors that were crops (main factor, n = 3) and compost amendment (sub-factor, n = 3). The crops were rice, soybean, and sesame and the sub-factors were cow manure plus rice straw compost, sugarcane compost, and no amendment. Soil samples were taken at harvest of the first crops in topsoil (0–10 cm) and subsoil (10–20 cm) in 2017 and 2018. In 2018, the abundance of free-living nematodes (FLN), which were dominated by bacterivores and fungivores, was greater in upland crops, while that of plant-parasitic nematodes (PPN) was greater in paddy rice. In particular, the density of the most predominant PPN genus, Hirschmanniella, was lower in upland crops than in paddy rice. Cultivation of sesame also reduced the number of the second predominant PPN genus, Bitylenchus, resulted in an increase in the ratio of the free-living to plant-parasitic nematodes. The diversity evenness index (J), Shannon-Wiener (H′) and Hill's indices increased in upland crops compared to those in rice fields in 2018. Crop rotation with sesame or soybean in a paddy field enhanced abundance and biodiversity of FLN and suppressed PPN and thus can be proposed for agricultural sustainability.