Cold water anomalies were found in the middle layer in the northern Taiwan Strait in the spring of 2015. The cold water was located at a depth of approximately 10–20 m, with warm water situated both above and below this cold water layer. This study investigated this phenomenon using a three-dimensional operational ocean model, in which the sea-surface net heat flux was justified by nudging the appropriate sea-surface temperature (SST) obtained from remote sensing data while maintaining a reasonable modeling skill level with respect to other parameters. The cold water anomaly phenomena were reproduced reasonably well in the model, and the mechanism can be determined by dynamic process analysis and thermal diagnosis of the model results. In the spring of 2015, when the northeasterly monsoon in the Taiwan Strait relaxed and changed to southwesterly, the offshore movement, which was related to both the geostrophic adjustment and Ekman transport in the upper layer, was supplemented by the bottom Ekman onshore transport at the lower level, which resulted in the presence of warm water at the bottom. Meanwhile, the increased solar radiation heated the water at the surface. In the model diagnostic analysis, such warming effects can be demonstrated by cross-strait horizontal advection and vertical diffusion, while in the middle layer, the warming effect was not particularly significant, which was the cause of the cold water anomaly.