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Typhoon (hurricane) is the most influential process of ocean–air interaction on the synoptic scale; it has a great influence on the heat exchange, mixing and ecological processes in the upper ocean, which in turn affect sea surface temperature (SST), leading to chlorophyll-a (Chl-a) concentration variation. SST is also an important factor affecting marine fishery resources. Chl-a is closely related to the marine ecosystem and primary productivity. In this study, we analyzed the response of SST and Chl-a to Typhoon Lekima (2019) process. The result indicates that the response of temperature to typhoon decreases from the center to the outer edge, which has a good correlation with the location, path and influence area of the typhoon center. The mean SST in the study area (14°~40° N, 116°~136° E) decreased during the typhoon’s passage, from 28.97 °C at the beginning (5 August) to 28.22 °C (15 August). The concentration of Chl-a was high in the northwest and coastal areas; its mean value in the study area decreased from 2 to 8 August (on 2 and 8 August, the concentration was 0.484 mg/m³ and 0.405 mg/m³, respectively). From 8 to 14 August, Chl-a decreased with the increase in SST, and 10 and 14 August were the two peak values of Chl-a (while SST was low). Chl-a concentration increased after the typhoon’s landfall (from 15 to 31 August); the Chl-a trend was the same as that of SST. The stronger the typhoon and the longer the residence time, the greater the contribution to the increase in Chl-a concentration at sea surface. Typhoon-induced rainfall over the ocean surface, increased evaporation of seawater, enhanced mixing within the mixed layer and upwelling of the pycnocline resulted in an increase in Chl-a quantity. This study describes the spatial response of the upper ocean to typhoons. It provides a general method for the comprehensive assessment of typhoons in marginal seas and upper open oceans, which has wide applicability and good scientific application prospects.