In this work, we investigated the geometrical structures, electronic and magnetic properties of S sites vacancy defects in heterostructure graphene/molybdenum disulphide ((HS)G/MoS2) material by performing first-principles calculations based on spin polarized Density Functional Theory (DFT) method within van der Waals (vdW) corrections (DFT-D2) approach. All the structures are optimized and relaxed by BFGS method using computational tool Quantum ESPRESSO (QE) package. We found that both (HS)G/MoS2 and S sites vacancy defects in (HS)G/MoS2 (D1S–(HS)G/MoS2, U1S–(HS)G/MoS2, 2S–(HS)G/MoS2 and 3S–(HS)G/MoS2) are stable materials, and atoms in defects structures are more compact than in pristine (HS)G/MoS2 structure. From band structure calculations, we found that (HS)G/MoS2, (D1S–(HS)G/MoS2, U1S–(HS)G/MoS2, 2S–(HS)G/MoS2 and 3S–(HS)G/MoS2) materials have n-type Schottky contact. The Dirac cone is formed in conduction band of the materials mentioned above. The barrier height of Dirac cones from Fermi energy level of (HS)G/MoS2, (D1S–(HS)G/MoS2, U1S–(HS)G/MoS2, 2S–(HS)G/MoS2 and 3S–(HS)G/MoS2) materials have values 0.56eV, 0.62eV, 0.62eV, 0.64eV and 0.65eV, respectively, which means they have metallic properties. To study the magnetic properties of materials, we have carried out DoS and PDoS calculations. We found that (HS)G/MoS2, D1S–(HS)G/MoS2 and U1S–(HS)G/MoS2 materials have non-magnetic properties, and 2S–(HS)G/MoS2 and 3S–(HS)G/MoS2 materials have magnetic properties. Therefore, the non-magnetic (HS)G/MoS2 changes to magnetic 2S–(HS)G/MoS2 and 3S–(HS)G/MoS2 materials due to 2S and 3S atoms vacancy defects, respectively, in (HS)G/MoS2 material. Magnetic moment obtained in 2S–(HS)G/MoS2 and 3S–(HS)G/MoS2 materials due to the unequal distribution of up and down spin states of electrons in 2s and 2p orbitals of C atoms; 4p, 4d and 5s orbitals of Mo atoms; and 3s and 3p orbitals of S atoms in structures. Magnetic moment of 2S–(HS)G/MoS2 and 3S–(HS)G/MoS2 materials is −0.11μB/cell and −0.29μB/cell, respectively, and spins of 2p orbital of C atoms, 3p orbital of S atoms and 4d orbital of Mo atoms have dominant role to create magnetism in 2S–(HS)G/MoS2 and 3S–(HS)G/MoS2 materials.