Marine heatwaves (MHWs) are period of extreme ocean temperatures that can last from a few days to several years. The increasing frequency and intensity of MHWs have devastating impacts on marine ecosystems. This study explores the characteristics of MHWs from 1982 to 2021 and their effects on chlorophyll (Chl) from 1998 to 2021 in the South China Sea (SCS), utilizing satellite data and reanalysis products. MHWs were classified into short-duration MHWs (SMHWs) and long-duration MHWs (LMHWs) based on their duration to analyze their effects. High-intensity and frequent MHWs were observed in the coastal regions of China, the western SCS (WSCS, average depth more than 200 m), and southwest of the Luzon Strait (LS, average depth more than 200 m). MHWs have increased by 14 days (R2 = 0.42, p < 0.01) and 0.99 times (R2 = 0.36, p < 0.01) per decade over the past four decades. The per-decade rate of increase is 44 % of the average MHWs days, and 36 % of the frequency in entire SCS.LMHWs contributed the most to this increase at a rate of 6.5 days (R2 = 0.43, p < 0.01) and 0.25 times (R2 = 0.45, p < 0.01) per decade. The trend of MHWs in the Pearl River estuary (PRE, On the coastal continental shelf, average depth <200 m) is noteworthy for cause for concern, increasing by 19 days and 1.4 times per decade.During SMHWs, the Chl response was relatively insignificant, with roughly 3 % negative anomalies across the entire SCS. However, LMHWs had a more profound impact on Chl,which decliend 8 % over the SCS, especially in the WSCS, PRE, and southwest of LS. During summer in the WSCS and winter southwest of LS, the negative anomalies of Chl varied between 20 % and 40 % of its daily climatology for each grid. In contrast, a noteworthy positive Chl response was observed in the PRE and adjacent waters during summer. The duration and intensity of MHWs in these regions affected Chl, and the suppression of Chl was more prominent as the intensity and duration increased, except in the PRE, where MHWs promoted Chl during both spring and summer. We identified various mechanisms by which MHWs impacted Chl in these regions, including weakened upwelling and eddies in the WSCS, changes in plume distribution along the PRE, and shallow mixed layer and weakened cyclonic circulation in the LS during winter. Our study underscores the need for immediate conservation measures to mitigate the effects of MHWs on marine ecosystems, particularly in the PRE and adjacent regions where harmful algal blooms (HABs) are a frequent and ongoing threat.