Offshore wind farms (OWFs) generate large-scale wind wakes, which might lead to upwelling/downwelling. Understanding the vertical marine response to the wake effects is crucial for assessing the ecological impacts of OWFs and optimizing their co-deployments with mariculture. In this study, we employ a high-resolution ocean model to investigate the spatiotemporal variations of upwelling and downwelling induced by the wind wakes of OWFs through idealized numerical experiments. We have two main findings. First, the wind-wake-induced upwelling and downwelling are not balanced in the north–south direction, resulting in a net effect of thermocline rising. Second, the thermocline depth changes caused by wind wakes develop nonlinearly over time. Specifically, when the elevated thermocline approaches the sea surface, the upwelling slows down significantly. The spatially asymmetric pattern of the upwelling is attributed to horizontal Ekman transport, while its temporal nonlinear evolution is caused by stratification changes. By utilizing the simulated change law of thermocline depth, we calculate the ocean response of OWF wakes in China’s adjacent waters. The results suggest that baroclinic theory overestimates the ocean response in the Bohai Sea, the Yellow Sea, and the nearshore waters of the East China Sea. However, in the open seas and the South China Shelf, the upwelling/downwelling is expected to be close to the theoretical calculations. This study provides a foundation for conducting regional simulations with high resolutions in areas where OWFs will be constructed.