A pot experiment was used to explore the distribution of fertilizer N and agronomic effects in a paddy soil-rice (Oryza sativa L.) system. Five treatments were set: without nitrogen, straw and inhibitor (C), urea (U), urea + straw (US), urea + urease + nitrification inhibitor (UI) and urea + urease + nitrification inhibitor + straw (UIS). Soil and urea-derived microbial biomass N increased significantly in US and UIS compared with straw-free treatments at seedling and tillering, indicating that biotic process play an important role in the retention of fertilizer N with straw addition. About 10% urea-N was recovered as fixed ammonium (FA) at seedling stage, subsequently released at tillering and maturation regardless of treatments, which emphasizes the importance of FA in the retention and supply of fertilizer N in paddy soils. Compared with U, rice yield and N uptake in US decreased by 7.8% and 25.2% respectively, while inhibitors (UIS) alleviated the reduction by 16.4% and 31.6%. The current research indicated UIS is recommended as the most appropriate management strategy in paddy soils of Northeast China based on N dynamics. But the economic effect as well as the field-scale validation need to be further evaluated.