In office buildings, an efficient design of windows and using light shelves as a passive design strategy significantly influence the thermal and visual comfort of occupants while enhancing the productivity and health of users. This study proposes a multi-objective optimization for the optimal design of windows and light shelves in office buildings to improve occupants' comfort. Initially, a parametric model was developed using Grasshopper parametric software. Afterward, the Honeybee energy and daylight plugin was employed for simulating thermal and visual conditions, and finally, multi-objective optimization was conducted with the Octopus plugin. This plugin can determine the best solution as a compromise decision for maximizing occupants' comfort. In this paper, an office building in Tehran has been chosen as a case study. The decision variables are window-to-wall ratio (WWR), shading control strategy, viewpoint, the transmission of glass, light shelf length, and light shelf height. The objective functions of the study are the annual average Predicted Percentage of Dissatisfied (PPD) and the annual average Discomfort Glare Probability (DGP). According to the results, the proposed optimization model leads to an 18.5–70.1% and 9.3–57.1% reduction in DGP and PPD indexes, respectively. The study findings provide practical and useful instruction for architects to select optimal specifications of windows and light shelves to develop occupants' thermal and visual comfort in office buildings.