An efficiency-oriented innovation analysis will enhance the understanding of the operational quality related to the transformation process of limited innovation investments for improving innovation outputs. The purpose of this study was to measure the static-dynamic efficiency of agricultural science, technology, and innovation (ASTI) and identify the efficiency determinants across the Group of Twenty (G20) countries. First, the static comprehensive efficiency of ASTI was measured employing the Data Envelopment Analysis (DEA)-BCC model, and some of the binding constraints to higher efficiency were investigated. Then, we applied the DEA-Malmquist index model to calculate the efficiency change of ASTI in certain periods and decomposed the sources of efficiency change. Finally, the G20 countries were classified into four-level clusters based on the rankings of efficiency measurement and capability evaluation of ASTI to locate the type of ASTI level and identify the type change in both the efficiency and capability. The empirical results indicate the following. (1) The efficiency range of the G20 developing countries was relatively larger than the G20 developed countries. The G20 developed countries showed a fluctuating downward trend, while the G20 developing countries showed an upward trend from the perspective of efficient proportion. The R&D expenditure redundancy and the agricultural journal papers deficiency were the main binding constraints to the higher efficiency of ASTI. (2) The total factor productivity change (TFPC) of ASTI showed an alternating trend of “decline–growth–continuous decline–growth recovery”, where the G20 developed countries experienced “growth–decline–growth” and the G20 developing countries underwent a fluctuating upward trend. The TFPC of ASTI in most G20 countries was primarily due to technological change. (3) The G20 developed countries usually had advantages in capacity, while the G20 developing countries performed better in efficiency.