The time projection chambers (TPCs) with triple GEM amplifiers are tested at HIMAC using 12C beams to investigate their nucleus track reconstruction capability. The two identical TPCs, each having an active volume of 96 × 64 × 144 mm3 and rectangular pixel pads, have been developed as prototypes of the LAMPS collaboration’s low-energy active target TPC (AT-TPC). The responses to light nuclei, such as particle identification and spatial resolution, have been investigated. The Si-CsI detectors located next to the TPCs further facilitate the identification of incident particles, as well as the matching tracks. This paper presents the technical details of the experimental setup, pulse shape analysis, tracking algorithm, and spatial resolution measurement. Comparisons of the experimental data with the calculations by the Monte Carlo (MC) simulation are also discussed.