In 2014—2015 and 2015—2016, a field experiment was conducted at Tongzhou Experimental Station of China Agricultural University, Beijing, to study the effects of nitrogen application frequencies on the yield and nitrogen utilization of winter wheat under fertigation with a center pivot system. The experiment set one time at jointing stage (T1), two times at jointing and filling stages (T2), three times at recovering, jointing and filling stages (T3), and four times at recovering, jointing, flowering and filling stages (T4), with consistency of irrigation and nitrogen rates during the whole growth period of winter wheat. The effects of nitrogen application frequencies on yield, ground biomass, plant nitrogen utilization, the grain protein content of winter wheat and the dynamic variation of soil nitrate content were evaluated. The two-year results showed that nitrogen application frequencies had a significant effect on the yield of winter wheat and the treatment T4 obtained the highest yield (9128.5kg/hm2 and 9092.3kg/hm2, respectively). No significant differences existed in total biomass of winter wheat between nitrogen application frequencies, while the distribution of biomass was affected significantly by nitrogen application frequencies in different growth periods. The treatment T4 greatly increased the harvest index, protein yield and nitrogen partial factor productivity of winter wheat. The soil nitrate content in depth of 0~40cm exceeded the average value when nitrogen was applied with low rates and high frequency during the whole growth period of winter wheat. Comprehensively, the fertilizer management of adopting base fertilizer and nitrogen application of treatment T4 was suggested during the growth period of winter wheat under center pivot irrigation system.