In wind resistance research involving super high-rise buildings, most studies have focused on increases in wind velocity with height. However, Ekman layer effects, which induce wind veering, have rarely been considered. The main objective of this study is to investigate the wind veering effects on square-section super high-rise buildings under various wind directions based on computational fluid dynamics (CFD). After a validation for the reliability of the numerical simulation method, large eddy simulations (LESs) are systematically performed on a 3D square cylinder with an aspect ratio of approximately 9:1. Simulated wind loads with and without wind veering under wind directions of 0°–75° are compared, and the flow mechanisms are discussed in depth. The results reveal that when wind veering is considered, the wind loads on square-section super high-rise buildings under certain wind directions (particularly in the range of 60°–75°) may be greater than those when wind veering is not considered under a 0° wind direction. More importantly, if the city in which the building will be located has a non-zero prevailing wind direction, the wind loads within the range of this non-zero wind direction may become controlling loads, which should be given sufficient attention by structural designers. • Performed LES of wind veering effects on a square-section super high-rise building under various wind directions. • Illustrated differences in wind loads with and without wind veering comprehensively. • Revealed underlying flow mechanisms of wind loads with and without wind veering.