Knee joint instability by anterior cruciate ligament(ACL) rupture is allowing the abnormal loading condition at the tibial epiphysis locally, resulting in producing locally different bone bruise. The study examined difference between local alteration patterns of trabecular bone microarchitecture at medial and lateral parts of the tibial epiphysis by ACL rupture. Fourteen SD rats were divided into Control(CON; n = 7) and Anterior Cruciate Ligament Transection(ACLT; n = 7) groups. The tibial joints were then scanned by in vivo ${mu}$-CT at 0, 4, and 8 weeks post-surgery. The results showed that alteration pattern on trabecular bone microarchitecture at medial part was significantly higher than that at lateral part of the tibial epiphysis in ACLT group from 0 to 8 weeks(P < 0.05). Tb.Th and Tb.Sp distributions were well corresponded with differences between aforementioned trabecular bone microarchitectural alteration pattens at medial and lateral parts of the tibial epiphysis in ACLT group from 0 to 8 weeks(P < 0.05). These findings suggest that the alteration patterns of trabecular bone microarchitecture should be locally and periodically considered, particularly with respect to the prediction of bone fracture risk by ACL rupture. Improved understanding of the alteration patterns at medial and lateral trabecular bone microarchitectures at the tibial epiphysis may assist in developing more targeted treatment interventions for knee joint instability secondary to ACL rupture.