Increasing frequency, intensity and duration of marine heatwaves (MHWs) are supposed to affect coastal biological production in different regions to different extents. To understand how MHWs impact coastal primary productivity and community succession of phytoplankton and assess the changes in resilience of phytoplankton communities, we conducted a mesoscale enclosure experiment simulating a marine MHW in the coastal water of southern China. After 8 days of the MHW (+3 oC) treatment, community biomass was significantly lower than the control’s, and primary productivity per volume of water was reduced by about 56%. Nevertheless, the phytoplankton community retrieved its biomass and primary productivity after the temperature was subsequently reset to that of the control. Although the MHW treatment decreased the abundance of diatom and increased the percentages of Synechococcus and Prasinophytes, the main phytoplankton functional types showed positive resilience that allowed the recovery of the phytoplankton community after the MHW. Our results indicate that key phytoplankton functional types in the southern coastal waters of China exhibited significant resilience, recovery, and temporal stability under the influence of the marine MHW by 3 oC rise. However, reduced primary productivity during the MHW period, along with decreased biomass density, might significantly influence secondary producers. In addition, the altered phytoplankton community structure may affect coastal food web processes at least during the MHW period.