To modulate the negative thermal expansion (NTE) performances of Sc2Mo3O12 ceramics, (NaZn)3+-substituted Sc2Mo3O12 ceramics were prepared via solid-state reactions. The crystal phase, morphology, and NTE properties of the NaxZnxSc2−x(MoO4)3 (0 ≤ x ≤ 1) samples were investigated. XRD results reveal that NaxZnxSc2−x(MoO4)3 samples undergo a change in crystal structure from orthorhombic to hexagonal phase due to (NaZn)3+ doping. (NaZn)3+ introduction also promotes grain growth and increases the density of the NaxZnxSc2−x(MoO4)3 ceramics. With the increase in (NaZn)3+ substitution, NaxZnxSc2−x(MoO4)3 ceramics exhibit stronger NTE, and the thermal expansion coefficients (CTEs) improve from −4.74 × 10−6 to −8.77 × 10−6 °C−1 in 30–650 °C. High-temperature XRD results reveal that the hexagonal NaxZnxSc2−x(MoO4)3 samples exhibit anisotropic NTE. With the increase in (NaZn)3+ substitution, the linear CTEs of the a and b axes decreased from −13.17 × 10−6 to −15.93 × 10−6 °C−1, while one of the c axes decreased from 18.38 × 10−6 to 12.27 × 10−6 °C−1. Consequently, hexagonal NaxZnxSc2−x(MoO4)3 samples present stronger NTE as the content x rises.