Water diffusion is a typical thermodynamic process in ambient aerosols that plays pivotal roles in their physicochemical properties and atmospheric lifetime and influences the climate and human health. A fair amount of aerosols become phase-separated after experiencing atmospheric aging processes such as efflorescence, amorphization, and liquid–liquid phase separation. However, detecting the hygroscopicity of heterogeneous aerosols is quite intractable. Here, for the first time, we directly characterized the water diffusion in single suspended phase-separated aerosols via a self-constructed laser tweezer Raman spectroscopy (LTRS) system. The H2O–D2O isotope exchange was harnessed to trace the water diffusion in single laser-levitated homogenous/heterogeneous microdroplets. The time-resolved cavity-enhanced Raman spectra of the microdroplets were used to detect the diffusion process in real time. Two archetypes of phase-separated aerosols, i.e., partially engulfed and core–shell, were studied. Moreover, we quantified the dynamic water diffusion process by experimentally measuring the diffusion coefficients. The results showed that compared with the homogenous aerosols, water diffusion limitations existed in the phase-separated aerosols. The incomplete diffusion may stem from the formation of certain hydrated molecule clusters. This work provides possible implications for the evolutions, especially the gas–particle partition, of the actual phase-separated atmospheric aerosols.