The risk of wind waves in a bay is often overlooked, owing to the belief that peninsulas and islands will inhibit high waves. However, during the passage of a tropical cyclone, a semi-enclosed bay is exposed to two-directional waves: one generated inside the bay and the other propagated from the outer sea. Typhoon Faxai in 2019 resulted in the worst coastal disaster in Tokyo Bay in the last few decades. The authors conducted a post-disaster survey immediately after this typhoon. Numerical modeling was also performed to reveal the mechanisms of unusual high waves. No significant high-wave damage occurred on coasts facing the Pacific Ocean. By contrast, Fukuura-Yokohama, which faces Tokyo Bay, suffered overtopping waves that collapsed seawalls. To precisely reproduce multi-directional waves, the authors developed an extended parametric typhoon model, which was embedded in the JMA mesoscale meteorological model (JMA-MSM). The peak wave height was estimated to be 3.4 m off the coast of Fukuura, in which the contribution of the outer-sea waves was as low as 10%–20%. A fetch-limited wave developed over a short distance in the bay is considered the primary mechanism of the high wave. The maximum wave occurred on the left-hand side of the typhoon track in the bay, which appears to be contrary to the common understanding that it is safer within the semicircle of a storm than on the opposite side. Typhoon Faxai was a small typhoon; however, if the radius was tripled, it is estimated that the wave height would exceed 3 m over the entire bay and surpass 4 m off the coasts of Yokohama and Chiba.