Abstract: In order to provide theoretical evidence for the management and fertilizer application in rain-fed agriculture, the experiment was conducted to study the distribution of soil moisture and the effect of nitrogen (N) and phosphorus (P) application on water use efficiency (WUE) and seed yield of oilseed flax under rain-fed conditions. The result showed that N and P fertilizers play an important role on soil water content under 100 cm depth. Compared with no P fertilizer application, the soil moisture of P application was higher in moderate N and high N treatment during seeding stage. The soil water storage was obviously higher in high nitrogen with P than no P application and increased by average of 4.38% , 3.37% and 3.66% , respectively. The rate of contribution of soil water based on a certain soil layer under N application or P application, however the rate of contribution of soil water moderated with N and P application in all soil layers. Seed yield of oilseed flax and WUE with high N combined with P treatment were obviously higher than other treatments, and seed yield and WUE was 1062.50 kg/hm2 and 2.60 kg/(mm·hm2), respectively. Seed yield and WUE increased by 8.12%- 16.76% and 7.31%-15.77% than other treatments.