Background: The thalamus and habenula are thought to be key brain regions in the etiology of major depressive disorder (MDD); however, few studies have investigated the structural connection between them. We compared the number of white matter tracts between the thalamus and habenula between patient with MDD and normal controls (NCs). Methods: The habenula and thalamus region of interest masks were extracted from brain magnetic resonance imaging data and individual tractography analysis was performed. First, we compared the number of fiber connections from the habenula to the thalamus between the MDD (n = 34) and NC (n = 37) groups and also compared hemispherical differences to investigate possible asymmetries. Results: There was a significant difference in the number of tracts in the right habenula-left mediodorsal thalamus pair between the two groups. For hemispherical fiber connections, the waytotal ratio of the right ipsilateral tract between the thalamus and habenula was significantly higher than that of the left ipsilateral tract in both groups. Conclusion: The number of right habenula-left mediodorsal thalamus tracts was higher in patients with MDD than in NCs. These results indicate that MDD is related to the disintegration of the left thalamus-right habenula tract function with an increased number of tracts as a compensational mechanism.