Significance Cyanobacteriochromes detect a broad range of light conditions to regulate various physiological processes in cyanobacteria. However, the initial photoinduced isomerization reaction in cyanobacteriochromes has not been well understood. The coupling motion of the excited chromophore with the local protein environment has not been carefully addressed and the often-observed multiphasic dynamic behavior was mostly attributed to the ground-state heterogeneity. Here, by integrating both femtosecond-resolved fluorescence and absorption methods, we revealed significant active-site solvation and thus elucidate a new molecular picture of photoisomerization, paving the way to explain many observations in cyanobacteriochromes and phytochromes.