We first observed the spin-to-charge conversion due to both the inverse Rashba-Edelstein effect (IREE) and inverse spin-Hall effect in a holey multilayer molybdenum disulfide (MoS2) intermediate layer in a Pt/YIG structure via LSSE measurements under nonequilibrium magnetization. We found an enhancement of approximately 238%, 307%, and 290% in the longitudinal spin Seebeck effect (LSSE) voltage, spin-to-charge current, and thermoelectric (TE) power factor, respectively, compared with the monolayer MoS2 interlayer in a Pt/YIG structure. Such an enhancement in the LSSE performance of Pt/holey MoS2/YIG can be explained by the improvement of spin accumulation in the Pt layer by induced spin fluctuation as well as increased additional spin-to-charge conversion due to in-plane IREE. Our findings represent a significant achievement in the understanding of spin transport in atomically thin MoS2 interlayers and pave the way toward large-area TE energy-harvesting devices in two-dimensional transition metal dichalcogenide materials.