Bubble dynamics are closely related to the electrochemical performance of a proton exchange membrane electrolyzer (PEMEC). However, tiny bubbles need to be clustered together to affect the electrochemical performance of PEMEC significantly. In this paper, the effect of microscopic bubbles on macroscopic electrochemical properties were assessed by bubble coverage. The bubble dynamics, two-phase flow, and electrochemical performance were captured under different conditions using a high-speed, microscopic visualization experimental system. The results show that various factors influence the two-phase flow pattern. At 60 °C, 1.5 A/cm2 and 5 mL/min, the annular flow occupied 76.8% of the gas phase area, and when the water flow increased to 80 mL/min, the annular flow ratio decreased substantially to 2.7%. The two-phase flow of bubbles in the flow channel showed different flow patterns over time. Under the experimental conditions (60 °C, 20 mL/min, 0.8 A/cm2), the bubble flow pattern experienced the emergence of bubbles, bubble flow, segmental plug flow, annular flow, and final steady state with the occurrence times of 0.15 s, 1.5 s, 5.0 s, 10.5 s, and 21.2 s, respectively. The bubble coverage increased with current density and temperature, while it decreased with the increase of water velocity. In addition, the effects of temperature and water velocity on bubble coverage and PEMEC performance vary in principle. Specifically, higher temperature mainly improves the bubble coverage by increasing the electrochemical performance of PEMEC. In contrast, higher water velocity mainly improves the electrochemical performance of PEMEC by decreasing the bubble coverage. This study elucidates the relationship between microscopic bubbles and macroscopic electrochemical performance, contributing to a better understanding of the processes and principles of bubble effects on the electrochemical performance of PEMEC. The results may provide a theoretical basis and experimental data for operating condition optimization, operating efficiency improvement, multiphase flow study, gas diffusion layer structure, and flow field design of PEMEC.