To explore the effects of different irrigation quotas and irrigation frequencies on winter wheat yield and grain quality under center pivot irrigation system, a field experiment on fertigation of winter wheat was carried out in 2014—2016 at Shunyi District, Beijing. Three irrigation treatments (W1, W2 and W3) were investigated with irrigation quotas of 135mm, 112.5mm and 90mm in 2014—2015, and 154.5mm, 132mm and 109.5mm in 2015—2016, respectively. Irrigations were applied at recovering-jointing stage, jointing-heading stage and heading-grain filling stage respectively, as the soil water content reached 70%, 75% and 75% of the field capacity, respectively. Each irrigation was sprayed at one time (C1) or at two times (C2) with equal irrigation amount at 9 d interval. The results showed that both the total water consumption and the average daily consumption of winter wheat from jointing to heading stage were the largest, and the highest yield was achieved under W1 treatment. The effects of the irrigation quota and irrigation frequency on water use efficiency were not significant in 2015—2016. The water use efficiency was decreased with the increase of irrigation quota, and the largest water use efficiency was 2.28kg/m3 at W3 treatment. Under the treatments of W1 and W2, the irrigation at two times can improve the spike number, yield and bulk density of winter wheat. The maximum yield was 9286.4kg/hm2 under the treatment of W1C2. The irrigation quota had more effect on wheat yield than irrigation frequency. Comprehensively, an effective method of irrigation was suggested for winter wheat in Beijing at recovering-jointing, jointing-heading and heading-grain filling stages with 45mm, 55.5mm and 54mm, respectively. Each irrigation could be applied equally at two times under center pivot irrigation system.