Longitudinal wheat yields in China have declined in recent times due to climate change, more frequent natural disasters, and suboptimal agronomic management. To date, it has been unclear which factors have predominated yield penalties realised hitherto in Hubei Province. This study aimed to identify key factors limiting wheat production across systems and agroecological regions, and provide a basis for increasing crop production while engendering food security. Survey data from 791 households in Hubei Province were analyzed using descriptive statistics and logistic regression. Significant spatial heterogeneity in average wheat yields was observed, with the Jianghan Plain region having significantly lower yields compared with the northwest region (yield gap: 1125 kg·hm−2). Dryland wheat had higher average yields than rice-rotation wheat (yield gap: 134 to 575 kg·hm−2). Socioeconomic factors, cultivation management measures, and environmental factors contributed differently to yield differences. Input costs and economic benefits were key social factors influencing wheat production. Variation in management were mainly attributed to planting methods, while soil fertility and climatic factors limited yields in some regions. In the northwest, low soil fertility and susceptibility to drought and high temperatures had greater influence on yields. In the Jianghan Plain, soil waterlogging and erosion were key challenges. Waterlogging increased the probability of low yields by 8.6 times, while severe soil erosion increased probability of yield loss by a factor of almost five. Low-yield farms in the Jianghan Plain were 21% higher than those in the northwest. Extreme weather events also contributed to low yields in the Jianghan Plain. We note significant potential for increasing farm-level wheat production in Hubei Province, with large existing differences across agro-ecological regions and planting modes. Differences in cultivation practices was a major driving factor of yield gaps between planting modes, while soil fertility and meteorological disasters drive regional yield differences. These results have implications for those aspiring to narrow the yield gap across regions and increase production of cereal crops.