Influenced by educational policies and newly emerging educational philosophies, the proportion of public space is expanding in primary and secondary schools in China. Consequently, the atrium in school design is increasingly drawing attention due to the consideration of space efficiency and its accommodability for diverse activities. Although many studies have already explored the daylighting performance of atriums, the particularities of primary and secondary schools are rarely noticed, which leads to the lack of a reliable basis for a quick judgment in the early design stage. This study used the annual daylight metrics of Spatial Daylight Autonomy (sDA300,50%) and Annual Sunlight Exposure (ASE1000,250 h) as the indicators, built a parametric model in Grasshopper, conducted the simulation using the Ladybug–Honeybee plug-in, and separately performed the linear regression analysis on the three groups of data from the different types of atriums. The results show that in Nanjing’s climate, the north and east sides of atriums are the most suitable orientations for classrooms, and a corridor width of 3 m ensures high-quality daylight for the bottom floors. The optimal design equations for atrium width and length are provided for the three types of atriums, respectively, hopefully, to ensure that classrooms surrounding the atrium can reach the requirement of sDA300,50% ≥ 0.75, and the design recommendations are offered based on the results.