The alterations in bone metabolism were associated with food and nutrition. Regrettably is that no studies have analyzed the bone microstructure subjected to complete fasting in mammals. Our study aimed to identify the effects and alterations of complete fasting on bones via histomorphometric analysis in adult female mice. Twelve-week-old C57BL/6J female mice were randomly divided into ad libitum (AL) and two-day complete fasting (FA) groups. Histomorphometry was carried out to analyze the differences in the microstructure of femurs after the experiment period. The histomorphometric data indicated that the bone resorption parameters, including the number of osteoclasts (Mu.N.Oc/B.Pm), osteoclast surface (Oc.S/BS), and eroded surface (ES/BS), were similar between the two groups. However, the bone formation parameters, including the number of osteoblasts (N.Ob/B.Pm) and osteoblast surface (Ob.S/BS), were markedly decreased in the FA group compared with the AL group. Thus, bone formation but not bone resorption was severely impaired following complete fasting. Furthermore, the osteoid surface (OS/BS) was observably reduced, which indicates that the bone mass should be reduced. However, there was no dramatic reduction in the osteoid thickness (O.Th); thus, the bone mass remained relatively stable between the two groups. These findings provide new insights in the increased incidence of osteoporosis in individuals on weight-reduction diets and other bone diseases associated with undernutrition.