Optical microcavities have become an attractive platform for precision measurement with merits of ultrahigh sensitivity, miniature footprint and fast response. Despite the achievements of ultrasensitive detection, optical microcavities still face significant challenges in the measurement of biochemical and physical processes with complex dynamics, especially when multiple effects are present. Here we demonstrate operando monitoring of the transition dynamics of a phase-change material via a self-referencing optofluidic microcavity. We use a pair of cavity modes to precisely decouple the refractive index and temperature information of the analyte during the phase-transition process. Through real-time measurements, we reveal the detailed hysteresis behaviors of refractive index during the irreversible phase transitions between hydrophilic and hydrophobic states. We further extract the phase-transition threshold by analyzing the steady-state refractive index change at various power levels. Our technology could be further extended to other materials and provide great opportunities for exploring on-demand dynamic biochemical processes.