As an emerging medical diagnostic technology, photoacoustic imaging has been implemented for both preclinical and clinical applications. For clinical convenience, a handheld free scan photoacoustic tomography (PAT) system providing 3D imaging capability is essentially needed, which has potential for surgical navigation and disease diagnosis. In this paper, we proposed a free scan 3D PAT (fsPAT) system based on a handheld linear array ultrasound probe. A global positioning system (GPS) is applied for ultrasound probes coordinate acquisition. The proposed fsPAT can simultaneously realize real time 2D imaging, and large field of view 3D volumetric imaging, which is reconstructed from the multiple 2D images with coordinate information acquired by the GPS. To form a high quality 3D image, a dedicated space transformation method and reconstruction algorithm are used and validated by the proposed system. Both simulation and experimental studies have been performed to prove the feasibility of the proposed fsPAT. To explore its clinical potential, in vivo 3D imaging of human wrist vessels is also conducted, showing clear subcutaneous vessel network with high image contrast.