Semimetal Bi in contact with monolayer MoS2 (mMoS2) as a substrate reduced contact resistance. This phenomenon has attracted widespread attention. Presently, systematic research on defects in semimetal-TMDs heterojunctions remains limited. In this paper, nine types of vacancy defects (three S-vacancies at the heterojunction interface (VSI, II, III), three S-vacancies on the top layer (VSI, II, IIIt), one Mo vacancy (VMo), Mo–S double vacancies (VMo–S) and Mo–S triple vacancies (VMo–2S)) and defect-free structure (Perfect) are designed in mMoS2. Their impact on defect formation energy, Interface charge transfer, and carrier mobility in three-layer (3L)Bi(0001)-mMoS2 heterojunctions are studied by the First-Principles. The energy analysis indicates that in the 3LBi-mMoS2 contact, VS are more prone to formation than VMo, VSt, VMo–S and VMo–2S. At the same time VSⅡ has the lowest formation energy under Mo-rich environments. The analysis of electron and charge redistribution in the 3LBi-mMoS2 contact with defects indicates that defect generation introduces peaks at the Fermi level, enhancing the hybridization of Mo_4d and S_3p. The hybridization rate of electron orbitals in VMo surpasses that in VS and VSt, signifying that heterojunction structures with defects exhibit increased electron injection efficiency at the interface compared to Perfect. The charge carrier mobility of S and Mo defects in 3LBi-mMoS2 reveals a significant reduction in the effective mass of charge carriers due to vacancy defects. Due to the location of defects, heterojunctions exhibit anisotropy. Obtain Perfect > VMo > VSII (370.7 > 277>125.1 cm2V−1S−1) for the x-direction carrier mobility (μx), while VMo > Perfect > VSII (440.8 > 279.7>131.6 cm2V−1S−1) for the y-direction carrier mobility (μy). These findings offer practical insights for utilizing defects to modulate the electronic properties of Semimetal-MoS2 heterojunction interfaces.