Currently sustainable development of the rice cultivation in China is confronted with a series of problems, among which high N fertilization rate and low use efficiency of N fertilizer is one. Pathways of N loss are closely related to transformation processes of the fertilizer after it is applied into the soil. A better knowledge and quantitative description of the transformation processes in paddy soil would help understand how N is lost in the rice-wheat rotation system. For that, a 2-year field experiment was carried out in a paddy field of alkaline paddy soil (Chaohuang Tu, pH=8.3) in Huai’an, North Jiangsu and a paddy field of neutral soil (Huangni Tu, pH=6.2) in Yixing, South Jiangsu to determine crop N recovery rate. At the same time, an in-lab aerobic incubation was conducted to reckon primary N mineralization and nitrification rates in the two paddy soils, using the ¹⁵N isotope dilution method, so as to further explain causes to the difference in N use efficiency between the two soils in the experiment. The field experiment shows that to achieve similar crop yields, the alkaline paddy soil required a higher rate of N fertilizer than the neutral paddy soil, but was lower in fertilizer N use efficacy (FNUE). The incubation experiment shows that, both the gross N mineralization and nitrification rates were higher in Chaohuang Tu than in Huangni Tu, which may be attributed to the higher pH in the former. Higher N mineralization and nitrification rates may lead to temporary accumulation of NO₃⁻-N, which can not be absorbed immediately by plants and then gets lost via a series of pathways. This may be one of the causes that lead to differences in FNUE between the two fields.