To identify the influencing factors of green production in Chinese grain and explore the effective pathways for achieving green and sustainable production of grain, thus ensuring the modernization of grain production in China, this research utilizes a three-stage DEA model based on nondesirable outputs. Using data from China’s land economic survey, the green production efficiency of 1810 land parcels is calculated by removing environmental factors and random disturbances. The random forest model is employed to rank the importance of factors influencing green production efficiency of grain, and the ISM model is utilized to analyze the hierarchy and associative pathways between factors. The following research conclusions are drawn: Firstly, environmental factors have an impact on green production efficiency of grain, and the use of the three-stage DEA model is necessary. From an overall perspective, there is still significant room for improvement in the average green production efficiency of grain, which stands at 0.76. Secondly, factors such as land contracting, land fragmentation, transportation accessibility, and land parcel size are important in influencing green production efficiency of grain. Specifically, land contracting and transportation accessibility have a positive impact on green production efficiency, while land fragmentation and land parcel size have a negative impact overall. Thirdly, the relationships between factors affecting green production efficiency of grain can be divided into four levels and three layers. There are five pathways of propagation, all of which have a common characteristic of influencing fertilizer usage, pesticide usage, and the quantity of self-owned machinery, thereby affecting green production efficiency of grain.