Photosystem II (PSII) catalyzes light-induced water oxidation through an Si-state cycle, leading to the generation of di-oxygen, protons, and electrons. Pump-probe time-resolved serial femtosecond crystallography (TR-SFX) has been used to capture intermediate states of light-driven enzymatic reactions. In this approach, it is crucial to avoid contamination of light into the samples when analyzing a particular reaction intermediate. Here, we describe a method for determining a proper light condition that avoids light contamination to the PSII microcrystals while minimizing the sample consumption in TR-SFX. With the proper illumination conditions determined, we analyzed the S2-state structure of PSII at room temperature, revealing the structural changes during the S1-to-S2 transition at an ambient temperature. By comparing with the previous studies performed at a low temperature or with a different delay time, we reveal the possible channels for water inlet and proton egress, as well as structural changes important for the water-splitting reaction.