The carbon balance of the farmland ecosystem depends on the fixed carbon content of crops and carbon emissions from soil heterotrophic respiration. In order to reveal the comprehensive effects of water and fertilizer levels on carbon balance in farmland ecosystems, a field experiment of summer maize/winter wheat rotation cycle in Yangling District of Shaanxi Province was conducted during 2015—2016. Three irrigation levels: high, medium and low (W1, W0.85 and W0.7 meant 90mm, 76.5mm and 63mm in summer maize season and 140mm, 119mm and 98mm in winter wheat season), four nitrogen fertilizer levels: high, medium, low and no nitrogen (N1, N0.85, N0.7 and N0 meant N 300kg/hm2, 255kg/hm2, 210kg/hm2 and 0kg/hm2 in summer maize season and 210kg/hm2, 178.5kg/hm2, 147kg/hm2 and 0kg/hm2 in winter wheat season) and four phosphate fertilizer levels: high, medium, low and no phosphate (P1, P0.85, P0.7 and P0 meant P2O5 90kg/hm2, 76.5kg/hm2, 63kg/hm2 and 0kg/hm2 in summer maize season and 150kg/hm2, 127.5kg/hm2, 105kg/hm2 and 0kg/hm2 in winter wheat season) were designed. CO2 flux measurements were performed, using the static opaque chamber and chromatography method, and aboveground biomass and yield were measured. The net primary productivity carbon fixation (CNEP) and soil microorganisms heterotrophic respiratory carbon release (CRm) were also calculated to evaluate net ecosystem productivity carbon fixation (CNEP). The results showed that the summer maize/winter wheat farmland ecosystem under different water and fertilizer treatments performed as carbon sink. The range of CNEP in summer maize and winter wheat seasons were 6805~7233kg/hm2 and 5842~6434kg/hm2, respectively. At high, medium and low fertilizer levels, with the increase of irrigation amount, the CNPP of summer maize/winter wheat rotation cycle was increased by 2.48%~ 5.96%, the CRm of soil was increased by 2.15%~15.20%, and the CNEP was increased by 1.16%~6.47%, respectively. Under the high, medium and low water supply levels, with the increase of fertilization amount, the CNPP of summer maize/winter wheat rotation cycle was increased by 2.95%~3.43%, the CRm of soil was increased by 5.23%~18.67%, and the CNEP was increased by 0.93%~2.79%, respectively. The increase of CNEP was negatively correlated with amount of irrigation. Under low water condition, compared with single application of nitrogen or phosphate fertilizer, combined application of nitrogen and phosphorus fertilizers, the CNEP of summer maize/winter wheat rotation cycle was increased by 4.86% and 7.34%, respectively. Variance analysis of the interaction of water and fertilizer was significant for the CNEP of summer maize/winter wheat rotation cycle. While water and fertilizer supply differed by 15% had a significant positive interaction with CNEP in winter wheat farmland. Combined application of nitrogen and phosphorus fertilizers and the coordinated supply of water and fertilizer were helpful to promote CNEP of summer maize/winter wheat ecosystem. Based on the principle of water and fertilizer saving, summer maize and winter wheat were beneficial to increase CNEP accumulation under W0.85N0.85P0.85 and W0.7N0.85P0.85 treatments, respectively.