Coastal lands are crucial arable land reserves that play a vital role in ensuring future global food security. In arable coastal lands, low soil quality often results in limited crop yield and soil organic carbon (SOC), making them promising sites for enhancing both soil carbon sequestration and agricultural production. However, a scarcity of long-term site experiments has led to a research gap regarding SOC sequestration in coastal arable lands, leaving potential uncertainties due to variations in planting systems, crop yields, and the influence of climate change. In this study, we focused on the Yellow River Delta (YRD) in China, which is a typical coastal agricultural area. We verified the adaptability of the Denitrifcation-Decomposition (DNDC) model in coastal farmlands based on an 11-year long-term observation experiment and continuous sampling survey data. We further explored the spatiotemporal changes of regional SOC stocks under two Shared Socio-Economic Pathways (SSPs) scenarios based on five Global Climate Models (GCMs) derived from the Coupled Model Intercomparison Project Phase 6 (CMIP6), along with three yield increase scenarios from 2020 to 2100. The results indicated that promoting single-cotton cultivation in coastal saline–alkali lands would result in at least 88.2% of farmland being converted into carbon sinks. In contrast, promoting the cultivation of a wheat–maize rotation system can promote regional SOC sequestration as a whole, with a maximum increase of 31.90 Mg C ha−1. By 2100, the SOC stocks decreased in cotton and wheat–maize rotation farmland by 3.9% and 11.6%, respectively, in the SSP585 scenario compared with that in the SSP126 scenario. Except for farmlands with wheat-maize rotation cropping system under the SSP126 scenario, the SOC stocks in all other scenarios are projected to reach their theoretical maximum values before 2050. Additionally, when reaching the North China Plain (S1) and national (S2) high-yield levels of farmland, the SOC stocks in cotton farmland by 2100 increased by 16.7% and 21.6%, respectively, whereas the SOC stocks in wheat-maize farmland increased by 1.8% and 4.8%, respectively. Our study revealed the mutually beneficial relationship between yield increment and SOC sequestration in coastal farmlands under climate change, as well as the potential for future SOC sequestration. We provided scientific support for land management and climate change mitigation strategic decision-making in coastal saline–alkali farmlands.