Knowledge of particle behaviors in laminar and turbulent flows is crucial for understanding the physics of natural processes and industrial applications, which is widely investigated in the multiphase mixing layers and jet flows. In contrast, the experiments concerned with particle transport in natural convection and coupled interactions between flow and particles are rare. In this study, comprehensive experiments were carried out in a water tank with a uniform heat flux applied at the bottom. The three dimensional (3D) motions of polystyrene particles are studied quantitatively based on a stereoscopic shadowgraph system. The stereoscopic shadowgraph system consists of two sets of conventional z-type shadowgraph configurations with two high-speed cameras. The 3D coordinates of single particles and particle groups are reconstructed using corresponding image coordinates and known camera calibration parameters. Then the trajectory and velocity are determined with 3D coordinates. In addition, particles and the flow motion in natural convection are qualitatively visualized by shadowgraph images, which allows to analyze the effect of flow motion on particle movement. It is observed that single particle moves in a wavy or circular path at small Rayleigh numbers, which is susceptible to other flow structures. Particles are entrained into the longitudinal vortex and moving in group of a jet shape at high Rayleigh number, in which the particles rise while circulating. The stereoscopic shadowgraph technique has been proved to be an effective tool to study particle motion in three dimensions, with the flow structures visualized at the same time.