Under the field experiment, two kinds of water management models were set up for controlling irrigation and flooding irrigation, and six nitrogen fertilizer levels of 0kg/hm2, 60kg/hm2, 85kg/hm2, 110kg/hm2, 135kg/hm2 and 160kg/hm2 were set up to study the effects of different nitrogen fertilizer and water regulation on carbon and nitrogen content and soil respiration in rice, at the same time, the rice yield of different treatments was determined to provide the countermeasure for the water and fertilizer pattern in cool area. The results showed that the content of carbon and nitrogen in different organs of rice and the soil respiration with control irrigation were larger than those with flood irrigation. The change of carbon content in different organs was similar but inconsistent, compared with control, with the increase of nitrogenous fertilizer, the amplitude of fluctuation was not significant（P>0.05). The results showed that with the increase of nitrogen fertilizer, the content of nitrogen were increased in different organs, that of the 135kg/hm2 and 160kg/hm2 treatments were significantly higher than that of other treatments （P<0.05), while that of the same treatment was decreased with the growing period. However, in the case of C/N in different organs, that of the 135kg/hm2 and 160kg/hm2 treatments was significantly smaller than that of other treatment （P<0.05). It was not conducive to the accumulation, metabolism and distribution of carbon and nitrogen in rice plants. According to the analysis of different soil respiration rates, the soil respiration rate of 110kg/hm2 treatment under two kinds of water treatment conditions was higher than that under other nitrogen fertilizer treatments. Under the precondition of considering yield synthetically, C110 treatment was the best coupling model of water and fertilizer, which should be paid attention to. The research result can provide scientific support for water saving and nitrogen reduction in the cold region of Heilongjiang Province.