This is one of the first empirical studies to estimate the technical efficiency of farmers’ flue-cured tobacco production, and explore the influencing factor of technical inefficiency on the perspective of within effects and between effects, aiming to provide a basic evaluation of farmers’ flue-cured tobacco production, and promote producers optimize their production. Results showed that the average technical efficiency level of flue-cured tobacco farmers was 0.7685; the scale elasticity was 2.67. Our study also revealed that the variation of farm household factors contributed 80.07% to technical inefficiency, and the other could be attributed to the variation of regional factors. Technical inefficiency of flue-cured tobacco production was significantly relative to producers’ education, planting scales, and planting years. In addition, regional disaster increased the possibility of technical inefficiency, while subsidies from flue-cured tobacco companies and government were to benefit reducing the technical inefficiency.