Water temperature is one of the most important factors that affect the occurrence of harmful algal blooms (HABs). Characteristics of sea surface temperature (SST) variability related to a Noctiluca scintillans bloom were analyzed with Himawari-8 data in the Beibu Gulf during mid-February 2021. An SST warming anomaly was found around the bloom area from 10:00 to 19:00 local time, with a peak temperature of 24.3 °C at 15:00, which was 2.9 °C higher than the surrounding normal sea water. The possible formation mechanism of the HAB-induced SST anomaly was studied in this work by integrating meteorological, ocean dynamics, and ecological processes. During the HAB event, the sea surface was covered by biological mucilage. A model that considered the net heat flux, heat capacity, density of seawater, and temperature variation was established to estimate the thickness changes (Δ H ) in the marine heating layer during the HAB event. The model results show that the heating layer thickness of the HAB area (Δ H between 0.76 m and 0.91 m) was smaller than that of the non-HAB area (Δ H > 1.19 m). The SST anomaly in this study might be caused by a thinner and warmer marine heating layer that is related to the biological mucilage on the surface of the HAB area.