The maxilla is generally acknowledged as being more trabecular than the mandible. Allograft currently available for use in the maxillofacial region is harvested from the hip and long bones, irrespective of their local characteristics, and grafted onto the jawbones. Other alternative are autograft or commercially available bone substitutes. Due to their inherent differences, an in-depth understanding of the bone microarchitecture is important to develop the most compatible graft for use at the maxilla. This cross-sectional study aimed to determine the microstructures of bone harvested from different sites of the maxilla, to be used for standard setting. Forty-nine specimens from seven human cadavers were harvested from the zygomatic buttress, anterior maxillary sinus wall, anterior nasal spine and anterior palate. Each bone block, measuring of 10 mm × 5 mm, was harvested using rotary instruments. Bone analysis was performed following micro-computed tomography to obtain trabecular number (Tb.N), trabecular separation (Tb.Sp), trabecular thickness (Tb.Th), and bone volume fraction (BV/TV). There were site-related differences, with BV/TV that ranged between 37.38% and 85.83%. The Tb.N was the lowest at the palate (1.12 (mm−1)) and highest at the anterior maxillary sinus wall (1.41 (mm−1)) region. The palate, however, had the highest trabecular separation value (Tb.Sp) at 0.47 mm. The TB.Th was the lowest at the anterior nasal spine (0.34 mm) but both the zygoma and anterior maxillary sinus regions shared the highest Tb.Th (0.44 mm). Except for having the lowest Th.Sp (0.35 mm), the anterior maxillary sinus wall consistently showed higher values together with the zygomatic buttress in all other parameters. Concurring with current clinical practice of harvesting autograft from the zygomatic buttress and anterior maxillary sinus wall, their bony characteristic serve as the microarchitecture standard to adopt when developing new bone graft materials for use in the maxilla.