Comprehending the relationship between spin and phonons is essential to regulate the lattice thermal conductivity in 2D magnetic materials. Lattice thermal conductivity is a relevant part to consider in magnetic data storage and the working of spin-based devices. In this article, we examined the origin and effect of spin–phonon coupling (SPC) on the lattice thermal conductivity of pristine CrI3 monolayer-based Janus monolayers Cr2X3S3 (X=Br,I). We find a high SPC in these Janus monolayers due to in-plane Cr–S atomic vibrations. We observe a reduction in the lattice thermal conductivity at Janus monolayer magnetic states (∼52.3% in Cr2Br3S3 and ∼63.9% in Cr2I3S3) compared to its paramagnetic states. The analysis is also conducted to determine which magnetic state has more anharmonicity using potential energy wells. A wide range of 2D magnetic materials can benefit from our results in the future development of spin-based thermal devices.