This manuscript demonstrates a multimodal imaging system which combined multiphoton microscopy (MPM) imaging modality with Fourier domain (FD) optical coherence microscopy (OCM) imaging modality. The system used a single fiber-based femtosecond laser as the light source for both MPM and OCM modality. The femtosecond fiber laser has a central wavlength of 1.03 μm, a pulse width of 120 fs and a bandwidth of 29 nm. The systems used fiber-based devices for both MPM and OCM imaging. The MPM and OCM shared the same excitation light path. The excitation light was delivered with the core of a dual-clad fiber. The MPM and OCM signal was collected by different parts of the dual-clad fiber. The MPM signal was collected by the clad of the dual-clad fiber and the OCM signal was collected by the core of the dual-clad fiber. The FD OCM used a home-built InGaAs detector array spectrometer with a maximum Aline speed of 7.7 KHz. The multiphoton signal collection efficiency was analyzed and several imaging modality including second harmonic generation imaging, two-photon excited fluorescence and optical coherent microscopy imaging were demonstrated.