Background The aim of this study was to analyze trabecular microarchitecture of augmented sinuses with hyaluronic matrix and xenograft by microcomputed tomography, and to investigate whether hyaluronic matrix has an effect on the newly formed bone quality. Materials and methods Thirteen patients undergoing maxillary sinus augmentation were included in this split-mouth study. Right and left sinus sites were randomly assigned to test and control group. In test group, the sinus was grafted with hyaluronic matrix and xenograft; in control group, only with xenograft. Four months after augmentation, bone samples were harvested during implant placement and analyzed for the following trabecular microarchitecture parameters using microcomputed tomography: bone volume (BV), total volume (TV), bone volume fraction (BV/TV), bone surface (BS), specific bone surface (BS/BV), bone surface density (BS/TV), trabecular thickness (Tb.Th), trabecular separation (Tb.Sp), trabecular pattern factor (Tb.Pf), and fractal dimension (FD). Results There was statistically significant difference only for BS/TV parameter between two groups. BS/TV was higher in hyaluronic matrix group compared with control group. Conclusions Addition of hyaluronic matrix to xenograft may enhance bone quality in terms of bone surface density. However, more research investigating the microstructural variation of augmented sinuses is needed with a greater sample.