The purpose of this study was to investigate degeneration-related ultrastructural changes of cartilages with molecular and biomechanical factors involved in matrix degradation under load. Immature pig front knee joints were used for experiments. Explant culture of the cartilage specimen were under compressive force with 30 MPa with 20% strain for 24 hours by FlexorCell. Control groups were prepared without loading. Structural study with Nomarski light microscopy and ultrastructural observation with scanning electron microscopy were performed. The analysis of chondrocyte apoptosis by TUNEL's method combined with corresponding view of phase contrast were performed as well. The immunochemical study of proteoglycan was investigated to show the matrix degradation. Our study demonstrated that the percentage of chondrocyte apoptosis was higher in the loaded cartilage than in the control group. A higher level of proteolglycan degradation was detected in the loaded cartilage compared to the control. The collagen fibrillar architecture of the loaded cartilage was shown to exhibit less interconnectivity under SEM investigation. This study has provided a new understanding of the way in which the chondrocytes and proteoglycans involved in the chondrocyte-matrix interaction, and how this relates to changes in fibrillar architecture under load.