The progress in stem cell research over the past decade holds promise and potential to address many unmet clinical therapeutic needs. Tracking stem cell with modern imaging modalities are critically needed for optimizing stem cell therapy, which offers insight into various underlying biological processes such as cell migration, engraftment, homing, differentiation, and functions etc. In this study we report the feasibility of photothermal optical coherence tomography (PT-OCT) to image human mesenchymal stem cells (hMSCs) labeled with single-walled carbon nanotubes (SWNTs) for in vitro cell tracking in three dimensional scaffolds. PT-OCT is a functional extension of conventional OCT with extended capability of localized detection of absorbing targets from scattering background to provide depth-resolved molecular contrast imaging. A 91 kHz line rate, spectral domain PT-OCT system at 1310nm was developed to detect the photothermal signal generated by 800nm excitation laser. In general, MSCs do not have obvious optical absorption properties and cannot be directly visualized using PT-OCT imaging. However, the optical absorption properties of hMSCs can me modified by labeling with SWNTs. Using this approach, MSC were labeled with SWNT and the cell distribution imaged in a 3D polymer scaffold using PT-OCT.