Rice morphology and N leaching, together with mineral N in the soil and soil solution around root, were determined at different growth stages in a 3-year experiment located in the Taihu Lake region, China. The results showed that the N application rates had little impact on the soil mineral N around root, but increased the dry matter and N accumulation aboveground in the high fertility soil (55.3 mg kg−1 of soil mineral N before rice season in 2008). However, no significant difference in grain yield was observed in all N treatments in these 3 years. Path analysis showed that spikelet per panicle made the greatest direct contribution (0.781) and total contribution (0.309) to grain yield compared to other yield components. And a higher panicle per m2 and dry matter accumulation resulted in yield decline later in the season due to a decline in the percentage of filled grains.