Multi-satellite and buoy observation data were used to systematically analyze the ocean response offshore of Taiwan to Super Typhoon Nepartak in 2016. The satellite data showed that a high sea surface temperature combined with a thick warm water layer and deep mixed layer provided a good thermal environment for continuous intensification of the typhoon. Two high-resolution buoys (NTU1 and NTU2) moored 375 and 175 km offshore of southeastern Taiwan were used to clarify the typhoon–ocean interaction as the typhoon approached Taiwan. The ocean conditions were similar at the two buoys before the typhoon, and both buoys were on the left side of the typhoon track and suffered similar typhoon factors (e.g., typhoon intensity and translation speed) during its passage. However, the ocean response differed significantly at the two buoys. During the forced period, the entire upper ocean was cooled at NTU1. In contrast, there was a clear three-layer vertical structure at NTU2 consisting of cool surface and deep layers with a warmer layer between the two cool layers. These responses can be attributed to strong upwelling of a cold eddy at NTU1 and vertical mixing at NTU2. These results indicate that, under similar preexisting conditions and typhoon factors, the movement of ocean eddies under typhoon forcing is an unexpected mechanism that results in upwelling and thus needs to be considered when predicting changes in the ocean environment and typhoon intensity.