In positron emission tomography (PET), parallax errors degrade spatial resolution. The depth of interaction (DOI) information provides the position in the depth of the scintillator interacting with the γ-rays, thus reducing parallax errors. A previous study developed a Peak-to-Charge discrimination (PQD), which can separate spontaneous alpha decay in LaBr3:Ce. Since decay constant of GSO:Ce depends on Ce concentration, the PQD is expected to discriminate GSO:Ce scintillators with different Ce concentration. In this study, the PQD-based DOI detector system was developed, which can be processed online and implemented in PET. A detector was composed of four layers of GSO:Ce crystals and a PS-PMT. The four crystals were obtained from both the top and bottom of ingots with a nominal Ce concentration of 0.5 mol% and 1.5 mol%. The PQD was implemented on the Xilinx Zynq-7000 SoC board with 8ch Flash ADC to gain real-time processing, flexibility, and expandability. The results showed that the mean Figure of Merits in 1D between four scintillators are 1.5, 0.99, 0.91 for layers between 1st–2nd, 2nd–3rd, and 3rd–4th respectively, and the mean Error Rate in 1D between four scintillators are 3.50%, 2.96%, 13.3%, and 1.88% for layers 1, 2, 3, and 4, respectively. In addition, the introduction of the 2D PQDs resulted in the mean Figure of Merits in 2D greater than 0.9 and the mean Error Rate in 2D less than 3% in all layers.