The rice root-knot nematode is increasingly widely distributed in China and has had a severe incidence in Hunan Province. It is thus necessary to investigate its population dynamics in paddy fields. This study was conducted to ascertain the effect of direct-seeded rice agroecosystems on the population dynamics of and root gall development in rice. The results indicated that the population density of in soil was markedly influenced by the agroecosystem, rainfall and temperature. The population density of J2, and eggs in the soil and root galls, were significantly larger in the dry aerobic rice agroecosystem and in the rain-fed upland agroecosystem than in the lowland double-rice cropping sequence agroecosystem. As it can affect soil moisture rainfall was the key factor affecting the density of nematodes in both the rain-fed upland agroecosystem and the dry aerobic rice agroecosystem. Field flooding was still an effective way to reduce the population density of . In addition, we observed that can lay eggs outside rice roots under laboratory conditions. Therefore, we propose a hypothesis that lays egg masses within roots when the soil moisture is high, but lays eggs outside when the soil moisture is suitable. By clarifying the population dynamics of in different types of direct-seeded rice agroecosystems, this study is conducive to controlling rice root-knot nematodes.