The high energy consumption of educational buildings in China has become a significant challenge in recent years. Atrium spaces offer abundant daylight and contribute to a pleasant and inviting atmosphere, are extensively used in university buildings. However, ensuring a comfortable indoor environment in the atrium while effectively reducing energy consumption remains a major challenge in the early process of design. This research identifies design variables that significantly affect the energy consumption and thermal comfort of atrium spaces and optimizes them simultaneously to establish a balanced strategy between them. This aims to offer a range of feasible design solutions for university teaching building design. Firstly, the study develops a typical atrium model for teaching buildings through a survey. Based on the Grasshopper platform, this model is simulated for energy consumption and thermal comfort. The study employs Energy Use Intensity (EUI) and Percentage of People Dissatisfied (PPD) as optimization objectives. Using the Octopus plugin, multi-objective optimization experiments are conducted on the typical atrium model’s design variables, leading to the development of a multi-objective optimization framework. The representative atrium design scheme is ultimately derived based on the Pareto optimal set of design parameters, providing a valuable reference for future teaching buildings design.