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Background: Mycobacterium tuberculosis induces cellular necrosis that could promote spread of infection. The aim of this study is to analyze the effects of Vitamin D3 supplementation to improve the effectiveness of 2nd-line anti-tuberculosis (TB) drug therapy, especially in relation with cell death pathways. Methods: Mus musculus C3HeB/FeJ was randomly divided into four groups containing eight animals each. The 1st group (G1), consisting of mice that were intratracheally infected with multidrug-resistant strain of M. tuberculosis and sacrificed on 2-week postinfection to confirm successful infection. (G2) was a group of TB mice without therapy. Then, (G3) was a group of mice with the 2nd-line anti-TB therapy. The last group (G4) was a group of mice receiving not only the 2nd-line anti-TB therapy but also daily oral Vitamin D3 supplementation. Immunohistochemistry was used to measure expression of nuclear Vitamin D receptor, apoptosis marker cleaved caspase-3, cathelin-related antimicrobial peptide (CRAMP) and LC3B autophagy markers, necrosis marker RIPK3, and collagenase matrix metalloproteinase-1 (MMP1). The number of bacteria in the lung was calculated by colony forming units. The partial least square structural equation modeling with SmartPLS 3.2.6 software was used to analyze structural models among the variables. Results: Supplementation of Vitamin D3 on the 2nd-line anti-TB therapy increases Vitamin D3 receptor, CRAMP, LC3B, caspase-3 (P = 0.026, P = 0.000, P = 0.001), presses MMP1, and the number of bacteria (P = 0.010 and P = 0.000, respectively). The structural equation modeling analysis shows that increasing autophagy pathways reduces necrosis by lowering MMP1, whereas apoptosis reduces necrosis by decreasing the number of bacteria (each with indirect effects - 0.543 and - 0.544). Conclusion: A comprehensive analysis with the partial least square structural equation modeling shows decreasing necrosis requires increasing autophagy and apoptosis. [ABSTRACT FROM AUTHOR]