The valley degree of freedom, besides charge and spin, can be used to process information and perform logic operations as well, with the advantage of low power consumption and high speed. The effective manipulation of valley degrees of freedom is essential for their practical applications in valleytronics and spintronics. In this work, the effective strategy is investigated for the valley manipulation of the WSeTe/CrI₃ van der Waals heterojunction with about 2% lattice mismatch by the first-principles calculations. The valley degree of freedom in WSeTe can be modulated by the magnetism of Cr atoms in the substrate via the magnetic proximity effect, including the vertical strain method and the rotation of the magnetic moments of Cr atoms. First-principles calculations are performed by using the VASP software package with the generalized gradient approximation functional in PerdewBurke-Ernzerhof (PBE) form. The spin-orbit coupling is considered when calculating the band structure to investigate the valley properties. The dependence of valley polarization on both vertical strain and the substrate’s magnetic moment direction has been systematically analyzed. There are two different stacking configurations for the WSeTe/CrI₃ heterojunction with Te/Se atoms at the interface, namely Te-stacking and Se-stacking. Although single-layer WSeTe does not have valley polarization, the Te-stacked and Se-stacked WSeTe/CrI₃ heterojunctions exhibit valley polarizations of 25 meV and 2 meV, respectively, which is influenced by spin-orbit coupling and the proximity effect of the magnetic substrate CrI₃, indicating the importance of the stack configuration. The Te-stacked configuration of the heterojunction has a larger valley polarization due to stronger orbital hybridization between W atoms in WSeTe layer and Cr atoms in CrI₃ layer. The application of vertical strain, which effectively tunes the interlayer distance, significantly regulates the valley polarization. Specifically, the valley polarization is increased to 59 meV when the interlayer distance decreases by 0.5 Å, while it decreases to 10 meV when the interlayer distance increases by 0.5 Å. Additionally, when the magnetic moment of the CrI₃ substrate rotates by 360°, the valley polarization changes between –25 meV and 25 meV. It reaches a maximum value when the magnetic moment is aligned along the out-of-plane direction. This study demonstrates that the valley degree of freedom in the WSeTe/CrI₃ van der Waals heterojunction can be effectively manipulated by adjusting the interlayer distance through vertical strain and by controlling the magnetic moment direction of the substrate. These findings provide valuable insights into the design and application of valleytronic and spintronic devices based on two-dimensional van der Waals heterostructures.