In order to explore the characteristics and rules of soil nitrogen change in paddy fields under the combined regulation of bio-organic fertilizers and controlled irrigation, a rice plot planting experiment was carried out. Two irrigation modes: flood irrigation (F), controlled irrigation (C) and three fertilization modes: full chemical fertilizer (A), replacement of chemical nitrogen by 15% bio-organic fertilizer (B), replacement of chemical nitrogen by 30% bio-organic fertilizer (C) were set up to analyze the variation characteristics of soil ammonium nitrogen content and soil nitrate nitrogen content during rice growth period. Every treatment is fertilized at the same nitrogen level. We found that till the tillering stage of rice, the average contents of ammonium nitrogen in treatments with bio-organic fertilizer under the same irrigation mode were all lower than those with full chemical fertilizer, with a decrease of 19.85%-48.78%; the average contents of nitrate nitrogen in treatments with C were lower than those with A, with a decrease of 15.35%-33.08%. While from the jointing stage, under the same irrigation mode, the average contents of ammonium nitrogen in treatments with bio-organic fertilizer were 12.71%-56.26% higher than those with full chemical fertilizer; the average contents of nitrate nitrogen in treatments with bio-organic fertilizer were also 19.21%-105.80% higher than those with full chemical fertilizer, except FB treatment. The soil nitrate nitrogen content in the whole rice growth period under controlled irrigation was significantly higher than that under flood irrigation (P<0.05), but the soil ammonium nitrogen content was higher under flood irrigation. The results show that bio-organic fertilizer combined with chemical fertilizer is beneficial to the accumulation of soil ammonium nitrogen and nitrate nitrogen after the tillering stage, and improves the accumulation of soil nitrogen in paddy fields, and the replacement of chemical nitrogen by 15% bio-organic fertilizer has a better effect. Moreover, controlled irrigation increases the content of soil nitrate nitrogen and reduces the content of soil ammonium nitrogen. For better environmental and economic benefits, a combination of controlled irrigation and replacement of chemical nitrogen by 15% bio-organic fertilizer is recommended.