A field experiment was conducted to investigate the effects of organic fertilizer replacing nitrogen of chemical fertilizer on transporting characteristics of soil carbon/nitrogen and wheat yield. The treatments included controlled release urea (CRU), organic fertilizer (OF) replacing 30%, 50% and 70% nitrogen dosage of controlled release urea, with the common urea (Urea) as the control. The results showed that the total biomass of organic fertilizer treatments were significantly increased by 13.83%~17.57%, the grain yield increased by 1.6%~10.5% compared with Urea. With the increase of replacing proportions of organic fertilizer, the increase effect on yield was reduced, and no significant difference was observed between 70%OF and Urea, but they were still significantly lower than the CRU treatment. The agronomic use efficiencies of CRU, 30%OF and 50%OF were significantly improved by 90.2%~124.4% compared with Urea. But there was no significant difference between 70%OF and Urea. The nitrogen partial productivity among organic fertilizer treatments and CRU showed no significant difference. With the increase of replacing proportion of organic fertilizer, the soil total carbon contents showed an upward trend, which was higher than CRU and Urea. However, the total nitrogen contents generally showed a downward trend with the increase of organic fertilizer. During the whole growth period, total nitrogen contents increased from sowing to regreening stage and then decreased. The total nitrogen contents of 30%OF were higher than those in other nitrogen fertilization treatments from grouting stage to maturity stage. With the increase of soil depth, the contents of nitrate nitrogen and ammonium nitrogen decreased. With the increased proportion of organic fertilizer, the nitrate nitrogen contents decreased, but ammonium nitrogen increased in each layer of soil (especially in the regreening period). Inorganic nitrogen contents in soil showed a declining trend during the whole growth period. However, compared with Urea, the nitrate nitrogen treated with organic fertilizer was mainly concentrated in the 0-40 cm soil layer, and the contents of ammonium nitrogen in 0-100 cm soil was higher than Urea and CRU (except seedling stage). Therefore, the application of 30%~50% organic fertilizer replacing nitrogen of chemical fertilizer, combined with controlled release urea, could significantly increase the contents of soil total carbon and ammonium nitrogen, reduce the nitrate nitrogen leaching in 60-100 cm soil, and improve the nitrogen use efficiency and grain yield of wheat.