The ridge–furrow rainwater harvesting (RFRH) planting mode is widely used in arid and semi-arid areas to solve the problems of agricultural water shortage and low productivity. However, the impact of film mulching on the stability of soil carbon pools makes this planting mode vulnerable to the risk of increased soil carbon emissions and carbon pool losses. In order to clarify the relationship between soil carbon emissions and hydrothermal factors, as well as the regulatory effect of biochar application on soil carbon sequestration and reduced emissions under this planting mode, we set up a biochar application experiment. The effects of the biochar application (at 10 Mg ha−1 biochar and 20 Mg ha−1 biochar) on the soil water dynamics, soil temperature changes, CO2-C and CH4-C flux dynamics, grain yield, carbon emission efficiency, and the net ecosystem carbon budget in wheat fields under the RFRH planting mode were investigated, with no biochar application as the control. The results showed that applying biochar increased the soil water content, soil average temperature, cumulative CH4-C uptake, wheat grain yield, and carbon emission efficiency by 3.10–12.23%, 0.98–3.53%, 59.27–106.65%, 3.51–16.42%, and 18.52–61.17%, respectively; reduced the cumulative CO2-C emissions by 7.51–31.07%; and increased the net ecosystem carbon budget by 2.91 Mg C ha−1 to 6.06 Mg C ha−1. The results obtained by equation fitting showed that in wheat fields under RFRH, the CO2-C emission fluxes had negative and positive exponential relationships with the soil water content and soil temperature, respectively, while the CH4-C uptake fluxes had no significant correlation with the soil water content and had an inverse U-shaped quadratic function relationship with soil temperature. Overall, these results suggest that the application of biochar to wheat fields under RFRH can improve grain yield, farmland carbon emission efficiency, and the net ecosystem carbon budget, and change wheat fields from a carbon source to a carbon sink. These results can provide a theoretical basis and technical support for efficient, green, and sustainable production in farmland in arid and semi-arid areas.