This study reports three dimensional (3 D) velocity profile measurements on planar domains of buoyant thermocapillary convection in thin layers of liquid using stereoscopic particle image velocimetry (PIV) to study the 3 D structure of thermocapillary convection associated with a hydrothermal wave (HTW). In addition, the experimental results were compared with 3 D numerical results obtained in this study to confirm the appropriateness of the periodic boundary conditions applied to lateral walls, which are frequently used in simulations. In our experiments and numerical simulations, a silicone oil with a Prandtl number of 16.1 was employed to form a liquid layer in a rectangular slot with uniform thickness. Consequently, the 3 D velocity profiles of the thermocapillary convection associated with HTW could be successfully reconstructed using stereoscopic PIV. Moreover, the experimental and numerical profile reconstructions were almost identical in a streamwise velocity; however, a spanwise velocity exhibited especially variations owing to the spanwise boundary conditions. Thus, the results of the current study suggested that spanwise walls could be introduced as the spanwise boundary condition for a more exact simulation of the thermocapillary convection related to HTW.