This study aims to analyze the spatial distribution characteristics and innovation efficiency of national agricultural science and technology parks (NASTPs) and identify the main influencing factors on the parks’ innovation and development. The goal is to optimize the allocation of science and technology innovation resources in these parks, promote national agricultural science and technology innovation, and enhance the quality of agricultural development. To achieve this, the paper employs spatial analysis methods and a three-stage DEA-Tobit model to conduct both macro and micro-level analyses. The research findings are as follows: (1) Distribution characteristics: NASTPs tend to exhibit a uniform distribution at the national scale, but at the provincial level, their distribution appears clustered and uneven. Specifically, three high-density areas and two sub-high-density areas have emerged on the eastern side of the Hu line, displaying a decreasing trend from east to west. (2) Innovation efficiency: By excluding the influence of environmental factors and random interference, the lack of scale efficiency (SE) emerges as the primary reason for the generally low innovation efficiency of NASTPs. (3) Environmental factors: Science and technology training exhibits a negative correlation with innovation efficiency in NASTPs. Leading enterprises, income level, innovation support, and demonstration and promotion show positive correlations with IE in NASTPs. To promote national agricultural science and technology innovation and enhance the quality of agricultural development, it is recommended, based on a central-level development perspective, to focus on the layout of the northeast and northwest regions. At the local level, expanding the scale of key enterprise inputs and increasing the demonstration and promotion of scientific and technological achievements are recommended. Additionally, at the NASTPs level, guiding the construction of a national agricultural high-tech industry demonstration zone is advised.