Higher water efficiency and higher carbon efficiency are important goals of sustainable agricultural development. However, long-term rotary tillage has a negative impact on soil, resulting in a reduction of soil water availability, and an increasing severity of water shortage for crop production. In addition to which China faces a sharp increase in global carbon emissions (CE), which are likely to rise even further as a result of current global warming trends. Subsoiling is an effective measure to improve soil surface structure; further, appropriate irrigation management can improve grain yield (GY). We conducted field trials in the North China Plain (NCP) from 2019 to 2021 to investigate the combined effects of 35 cm subsoiling (S) and rotary tillage to a 15 cm depth (R), in combination with no irrigation (I0), 60 mm irrigation only at jointing (I1), or 60 mm at jointing and 60 mm at heading (I2), on crop water productivity (CWP) and CE during winter wheat production. Compared with R, S significantly increased soil water storage (SWS) (4.44%) and CWP (33.01%). Although S increased CE (17.94%), soil carbon storage (C_stock) (7.37%) and carbon accumulation rate (C_acc) (32.98%) were significantly higher than that R. The effect of irrigation was significant, and treatment effects on SWS, GY, and evapotranspiration (ET) were as follows: I2 >I1 >I0. The optimal treatment for GY in 2019–2021 was S-I2, but CE (2.92%) of S-I2 was higher than that of S-I1. Carbon emission efficiency (CEE) and C_acc of S-I2 and S-I1 were at a high level and no significant difference between them was observed. CWP under treatment S-I1 was significantly higher than for any other treatment. These results suggest that subsoiling to a depth of 35 cm in combination with 60 mm irrigation at jointing improved CEE and CWP of winter wheat in the NCP.