Objective To preliminarily explore the feasibility of tree shrew as a new kind of animal model in research of amblyopia, to discuss the primary visual cortex plasticity mechanism of form deprivation in tree shrew, and to provide a theoretical basis for further understanding the mechanism of amblyopia formation and recovery. Methods Sixty 30-days old tree shrews were divided into five groups, 12 in each group: the group A had the right eye sutured for 1 month; the group B had the right eye sutured for 2 months; the group C had the left eye sutured for 1 month and then opened and the righ eye was sutured for 1 month, in other words, the group C was performed by alternating suture; the tree shrews of control group 1 (D1) were in the same age as the the group A, but fed in normal breeding environment; the tree shrews of control group 2 (D2) were at the same age of groups B and C, but fed with a normal diet. Samples of the visual cortex were taken after the completion of modeling, and were processed to observe the histology and ultrastructure of the visual cortex, the neuron apoptosis, and the c-fos protein expression in the tree shrews of different groups. Results Damages to different degrees were found by histological and electron microscopic examination of the visual cortex in each experimental group, and they were more obvious in the group sutured for 2 months. TUNEL staining showed that there were no significant differences between the apoptosis in the experimental and control groups. The expression of c-fos mRNA and protein in the experimental groups was decreased, and it was the lowest in the group sutured for 2 months. There was a small increase in the c-fos expression after the alternate suture, and no significant difference of c-fos expression was found in the control groups. Conclusions Different degrees of deprivation amblyopia lead to different histopathological changes. There is a plasticity in the neurons affected by amblyopia. Tree shrew can be used as an ideal animal model for the studies of form deprivation amblyopia.