As the growing population and the environment deterioration worldwide, it is a great challenge to explore how to use the available cropland and resource to feed more people with less environmental cost. Here, we performed a planting survey about winter wheat involving 1496 smallholders across the Huang-Huai-Hai Region. Based on this survey, we summarized the farmers' cultivation pattern (FP). By water and fertilizer coupling effects, we proposed a lower carbon-emission pattern (T1) and an equal carbon-emission pattern (T2). FP treatment included 270–330 kg ha−1 nitrogen (N), 120 kg ha−1 P2O5, 120 kg ha−1 K2O and irrigated once - three times; T1 treatment included 180–240 kg ha−1 N, 120 kg ha−1 P2O5, 80–120 kg ha−1 K2O, 0–15 kg ha−1 ZnSO4 and irrigated once - twice; T2 treatment included 240–300 kg ha−1 N, 120–180 kg ha−1 P2O5, 120–150 kg ha−1 K2O, 15–30 kg ha−1 ZnSO4 and irrigated once - three times. A 4-year cultivation experiment was conducted in 10 cities. The results showed that T1 and T2 treatments exhibited similar positive effects in promoting sustainable intensification in the region compared with FP. Compared with FP treatment, T1 and T2 increased the yields by 10.0% and 19.6%, water use efficiency by 19.8% and 15.2%, and partial factor productivity from applied N by 48.4% and 20.4% in the region, respectively; meanwhile, T1 treatment decreased carbon emissions by 25.2%. The yield of T1 and T2 treatments was higher than that of FP, mainly due to increased spike number, dry matter accumulation, and harvest index, which may be affected by the lower proportion of nitrogen fertilizer in the applied water and fertilizer. To facilitate sustainable intensification in the region, encouraging local farmers to adjust applied nutrients and water structures for lower carbon emissions will be a universal orientation. This research provides a reference for other similar regions.