Fast switch between pulses of sufficient energy but different wavelengths plays an important role in fast functional photoacoustic imaging. Commonly used Stimulated Raman scattering through a long optical fiber can produce multiple wavelengths, but longer fiber means lower energy, which would decrease image quality. Shorter optical fiber is thus more desired for fast imaging. However, it should be noted that too short pulse separation may generate photoacoustic signals that are temporally overlapped. Here, we propose an approach to solve this overlapping problem in ultrafast PA imaging using a Fourier-domain based method. The validity of this method is confirmed through simulation firstly, and then it is applied to separate overlapped PA signals. Lastly, in vivo OR-PAM mapping of mouse ear’s sO2 photoacoustic imaging is achieved.