Forests are the most important renewable resources and provide critical ecosystem services worldwide, especially the provisioning service, making a great contribution to human well-being. The Three-North Shelter Forest Program (TNSFP) is a large-scale ecological project aimed at improving ecological environments and consolidating economic construction in China through the development of artificial forests. In our study, stochastic frontier analysis was adopted to estimate forest production efficiency (FPE) by using dynamic panel data. Based on the FPE of 13 provinces located within the TNSFP region during the period 2000–2016, the effects of the natural and socioeconomic influencing factors on FPE were further explored by using the Tobit regression model. The estimated results confirmed the validity of the constructed model and revealed an increasing trend of the mean annual FPE value, which ranged from 0.3147 in 2000 to 0.5681 in 2016. The FPE was declining from the eastern region to the western region in 2000. However, this spatial distribution characteristic changed enormously in 2016; regions with low FPE were in the center of the TNSFP region, surrounded by the regions with high FPE. Moreover, the following factors positively influenced FPE: average temperature (1.4476), total annual rainfall (0.0800), per capita GDP (0.0882), the education levels of forestry employees (0.2120), the number of forest technology stations in townships (0.0149), and disease and pest control areas (0.0190). However, the impacts of the policy relating to the Natural Forest Protection Program on FPE were insignificant. These influencing factors had differential effects on FPE within the TNSFP’s three sub-regions during the period 2000–2016. These findings can contribute to more efficient forest management and strengthen resource and environment management.