As part of the next generation PET project, uniformity of full energy pulse height for all crystal elements was improved in the depth of interaction (DOI) detector constructed of three-dimensional crystal arrays. In our previous report, we found that the DOI detector constructed of four stages of a 2 × 2 Gd2SiO5:Ce (GSO) crystal array provides good crystal identification performance but poor uniformity of the energy pulse height distribution. The upper stage crystal elements which stay further from the photocathode of a PMT have a tendency to show lower energy pulse height. For example, the ratio of the full energy peak of the top stage crystal to the bottom stage one was about 0.3. We designed a new DOI detector improved in the uniformity. By optimizing crystal surface finishes, reflector configurations, and optical coupling between crystal elements, we got comparable energy pulse height from the upper stage crystals to the bottom stage crystals. Despite this change of detector conditions, good separation between each area corresponding to crystal elements is maintained on two-dimensional histograms obtained by Anger-type position calculation. The uniform full energy pulse height of every stage crystal allows a narrower dynamic range of the electrical circuits, and may give a great advantage in getting an accurate scatter correction. It also improves energy and timing resolution.