In the present study, morphological and mechanical characteristics in caudal vertebrae of rats with calcium free diet (CFD) were detected and tracked to investigate the correlation between bone metabolism and calcium deficiency, using micro-computed tomography (micro-CT) and finite element (FE) analysis. Twelve female Sprague Dawley rats (12 weeks old) were randomly divided into two groups, CFD and normal groups. The rats were observed from 0 week (just before starting CFD) to 8 weeks. Structural parameters, bone mineral density (BMD) and effective modulus were measured and calculated. There was more significant age-related decrease of BV/TV, Tb.Th and Tb.N in CFD group than in normal group, whereas more significant increase of Tb.Sp and SMI was found in CFD group than in normal group. In CFD group, BMD of trabecular bones decreased. However, there was no change in that of cortical bones from 0 week (just before starting CFD) to 8 weeks. In the simulated compression test using FE models, the structural modulus of CFD group was smaller than that of normal group. In conclusion, CFD led to bone loss and decreased bone strength in the rat caudal bones.