Changes in the lignocellulosic structure of oil palm empty fruit bunches (OPEFB) during composting treatment using an in-vessel composter was investigated in this work. The composting process was completed within 40 days of treatment, and the final C/N ratio achieved was 13.85. Scanning electron microscopy (SEM) revealed that the structure of OPEFB material was severely degraded, especially during the thermophilic phase where the biodegradation process was most active. Close examination of the physicochemical and thermal analysis using X-ray diffraction (XRD), Fourier transform infrared (FTIR), and thermogravimetric and differential thermal analysis (TG/DTA) showed that the crystallinity size of the OPEFB structure decreased. This result was attributed to the removal of silica bodies from OPEFB materials. Also, the functional groups of cellulose, hemicelluloses, and lignin structures had changed throughout the composting period, and the most extensive degradation of cellulose was detected in the thermophilic phase. It was also found that the exothermic peak of the matured compost reduced most significantly compared to the raw OPEFB. In conclusion, the in-vessel composting system was able to enhance the degradation process of OPEFB materials for producing compost.