FRET has been used as a powerful tool in biological fields as biosensors, bioimaging, protein folding/unfolding monitoring, biomolecular interactions, and so on. It is also important to applying FRET to high hydrostatic pressure studies on biosystems or biorelated systems. Herein, we construct a FRET system by labeling Cy3 on C-phycocyanin (C-PC) to investigate the effect of hydrostatic pressure on the fluorescence and FRET behavior between them. The fluorescence spectra of individual Cy3, C-PC, and integrated Cy3/C-PC system are measured separately under compression. An enhanced FRET efficiency under compression is concluded based on fluorescence behavior differences between them. To further reveal the origination of the enhanced FRET efficiency with pressure, the overlap integral between Cy3 emission and C-PC absorption is also calculated, and several possible explanations are proposed.