Abstract This study uses observations from two semi-Lagrangian EM-APEX floats to investigate how rain layers (RLs) influenced near-surface ocean stratification and sea surface temperature (SST) warming in June 2023. A RL, likely formed by precipitation prior to the field experiment at the edge of a warm eddy, induced strong salinity stratification around 40 m depth on yearday 169. From the floats’ initial passage over the intersected points (yearday 169) to their return (yearday 175), the SST increased by over 1 °C, accompanied by a salinity increase of 0.2 psu in the upper 20 m. Using the heat budget approach, we identify surface radiative flux as the primary driver of upper ocean warming. In the ocean interior, the RL suppressed the penetration depth of nighttime convection, reducing the entrainment of cooler water from below. This pre-existing salinity stratification allowed the surface heat to accumulate, favorable for the restratification of the temperature structure in the upper 40 m over subsequent days. Although the RL was weakened by the strong horizontal salinity advection after yearday 173, the increased temperature stratification continued to restrict nighttime convective mixing in the upper 15 m. These results highlight the important role of transient rain-induced stratification in amplifying SST warming under calm, clear-sky conditions and offer valuable insights for improving SST prediction in complex air–sea interaction processes.