The incorporation of skylights significantly improves indoor natural lighting uniformity and illumination levels. Additionally, the use of an air layer helps mitigate hear transfer between indoor and outdoor environments, thereby improving the overall quality of the indoor light environment. Using a comprehensive market building in Handan City as a case study, this research designs a double-layer skylight transmission system comprising 27 combination configurations by integrating skylights and air layers through the Grasshopper simulation platform. With the help of Octopus, a multi-objective optimization solution is developed to balance energy consumption and light comfort. The independent variables and evaluation index datasets are further analyzed using the Hiplot platform to evaluate correlations between design parameters and light environment indicators. Results show that the optimal configuration is achieved when the air layer thickness is 0.8 m, the semi-transparent material thickness is 0.005 m, and the skylight area ratio is 0.3. Under these conditions, the proportion of indoor effective daylight illumination increases by 10.97%, the probability of daytime glare decreases by 39.40%, the brightness ratio between north-south entrances and exits and their background surfaces decreases by 61.45% and 45.10% respectively, and energy consumption per unit area is decreased by 18.42%. Correlation analysis reveals that interlayer height is negatively correlated with daylight coefficient, effective daylight illumination, and daytime glare probability, although these correlations are weak. The skylight area ratio is negatively correlated with indoor effective daylight illumination, while the thickness of the interior light-transmitting panel is positively and strongly correlated with daytime glare probability. Finally, the system’s economic viability, applicability, and feasibility are analyzed, offering a novel design approach and component model for enhancing the indoor light environment of large-scale public buildings in urban settings.