Adjusting the planting structure, as a key intervention in agricultural ecosystems, plays a vital role in enhancing ecosystem service value (ESV) and improving system functionality. This study evaluated the farmland ecosystem service value (FESV) of Chinese counties using the equivalent factor method, and analyzed the spatio-temporal differentiation of planting structure and FESV. Spatial correlation tests confirmed the spatial dependence and heterogeneity between the two. The single-region and two-region spatial models were employed to examine the direct effects of planting structure on FESV, as well as its spillover gradients and underlying mechanisms. The results showed that: (1) The planting structure of China’s three major grains generally exhibited a pattern “higher in the east and lower in the west”, while FESV distribution aligned with the “Heihe-Tengchong Line”, with the highest contribution from regulating functions, followed by provisioning, supporting, and cultural functions. (2) Both planting structure and FESV displayed significant spatial agglomeration. Adjusting the planting structure not only improved local FESV but also affected neighboring regions through spillover effects, primarily manifesting as negative competitive effects. (3) The two-region model revealed consistent positive FESV spillover effects across various regions, including “National Key Ecological Function Area”, “China’s Major Grain Producing Area”, and “National Urban Agglomerations”, though with notable asymmetry between regions. (4) The spillover effects on FESV were especially pronounced in areas with lower grain-planting proportions. Therefore, we should pay more attention to the ecological benefits of planting structure adjustments and its asymmetric spillover effects, to ensure the health and sustainability of agricultural ecosystems, to promote mutually beneficial economic and environmental cooperation between regions.