This study investigated the offset effect between green manure (GM) application and plastic film mulching (PFM) on soil organic carbon (SOC) stock change during maize cultivation. Within PFM and no-mulching treatments, three different fertilization sub-treatments were applied: (a) chemical fertilizer, (b) barley and (c) hairy vetch. The SOC balance were evaluated by analyzing the net ecosystem carbon budget (NECB). The results showed that the NECB value was negative during maize cultivation regardless of mulching or fertilization condition, indicated SOC loss. The PFM increased maize yield (P < 0.001) by improved soil moisture and temperature. Crop growth was enhanced under PFM relative to no mulching by 23–26%, 16–25% and 1–8% in the sub-treatments, respectively. However, PFM significantly increased carbon losses by 26–29%, 103–107% and 60–62% over no mulching in each fertilization, respectively (P < 0.001). the temperature sensitivity of CO2–C loss was 52–70% higher in PFM than that in no mulching. Accordingly, the NECB was 1.3, 5.6 and 3.0 times lower with PFM relative to the no-mulching value in the three fertilization, respectively. Under no mulching, GM application reduced SOC loss by 33–59% compared with NPK, while under PFM, it accelerated SOC loss by 8–48%. Barley showed the smallest NECB decrease (− 1.0 Mg C ha−1) under no mulching and the largest NECB decrease (− 5.7 Mg C ha−1) under PFM. The findings indicate that GM application is not enough to sustain SOC stock under PFM and suggest that the additional recycling of crop residue, such as maize stover, is necessary to increase the soil C stock.