Molybdenum disulfide (MoS₂) films are promising solid lubricants for aerospace and other advanced applications, yet their tribological performance is highly sensitive to environmental conditions. To enhance environmental adaptability, Zr-doped MoS₂ composite films were prepared by magnetron co-sputtering, and their composition, microstructure, mechanical properties, and tribological behavior were systematically investigated. The results showed that the as-deposited MoS₂ films exhibited a nearly stoichiometric sulfur-to-molybdenum ratio (S/Mo ≈ 2), while the Zr-doped MoS₂ composite films showed sulfur-deficient, sub-stoichiometric ratios (S/Mo < 2). Pure MoS₂ films displayed a porous columnar structure, whereas with the incorporation of Zr, the columnar structure becomes progressively more compact. Moreover, the film structure transitions from a purely crystalline form to a two-phase structure with both crystalline and amorphous phases coexisting. The hardness and elastic modulus of the films increased with the addition of Zr, mainly due to the densification of the structure and the disorder introduced in the film. Moderate Zr doping markedly improved the friction and wear performance of composite films across vacuum, atmospheric, and humid environments. The optimal film achieved a coefficient of friction (COF) of 0.02 and wear rate of 6.23 × 10⁻⁸ mm³/N·m in vacuum and COFs of 0.10 with low wear rates in both atmospheric and humid conditions. By adjusting the Zr target power to modulate Zr content, the crystallographic orientation and microstructure of MoS₂-Zr composite films could be tailored, thereby regulating their mechanical and tribological properties. This study provides theoretical guidance for the application of metal-doped MoS₂ composite films under alternating environmental conditions.