pH influences excitation-energy-relaxation processes in photosynthetic light-harvesting complexes. Here, we report the excitation-energy dynamics by pH changes in fucoxanthin chlorophyll a/c-binding proteins (FCPs) isolated from a diatom Phaeodactylum tricornutum, probed by time-resolved fluorescence spectroscopy at 77 K. The fluorescence curve measured at pH 5.0 showed a shorter lifetime component than that measured at pH 6.5 and 8.0. The rapid decay component at pH 5.0 is supported by fluorescence decay-associated (FDA) spectra, where strong fluorescence decays relative to fluorescence rises appear in the pH-5.0 FDA spectrum with 70 ps. These results indicate that the diatom FCPs switch their function from light-harvesting to energy-quenching via arrangements of the energy-transfer pathways under acidic pHs. Based on the crystal structure of the diatom FCPs, we propose a model for the energy-quenching machinery through structural changes of the pigment environments, thus providing insights into the pH-dependent light-harvesting strategy in the diatom FCPs.