The aim of this study was to identify an efficient agrophotovoltaic (APV) system structure for generating electricity from solar radiation without causing an adverse impact on crop growth. In a temperate climate region, it is critical to design an APV system with appropriate structure with the maximum amount of electricity generation because, unlike in desert areas, strong solar radiation is only available for a few hours a day. In this study, APV systems with three different shading ratios (i.e., 32%, 25.6%, and 21.3%) were considered, and the optimum structure in terms of electricity efficiency and profitability was investigated via nonlinear programming. Moreover, an estimation model of electricity generation was developed via a polynomial regression model based on remote sensing data given by the APV system located at Jeollanamdo Agricultural Research and Extension Services in South Korea. To evaluate the impact of the APV on crop production, five different grain crops—sesame (Sesamum indicum), mung bean (Vigna radiata), red bean (Vigna angularis), corn (Zea mays), and soybean (Glycine max)—were cultivated in the system. As a result, the proposed optimization model successfully identified the best APV system structure without reducing existing crop production.