Effectively suppressing lattice thermal conductivity is a critical step for improving the thermoelectric performance. Taking open framework Si24, a potential thermoelectric material and a newly synthesized cage-like Si allotrope, as an example, we systematically investigate the lattice thermal conductivity of this new structure filled with alkaline-earth guest atoms ([email protected]24, X = Mg, Ca, Sr, and Ba) by combining first-principles calculation and phonon Boltzmann transport theory. The calculated lattice thermal conductivity is obviously decreased as guest atoms are inserted in the void sites of the Si24 framework, which is a common phenomenon for the guest-host systems. However, it is surprising to find that the thermal conductivity of this new filler structure presents a prominent element dependency. Inserting Ca into Si24 framework generally leads to 3 to 10 times lower thermal conductivity than that with other alkaline-earth atom fillers, and the value along zz crystal direction of 0.59 W/mK is even lower than that of amorphous silicon, despite the intrinsic thermal conductivity of pristine Si24 is as high as 21.25 W/mK. Such ultra-low thermal conductivity is found to be closely related to the strong harmonic interatomic interaction among guest and host atoms of [email protected]24 system. The strong interaction gives rise to anomalous contraction effect on the Si24 lattice (the volume abnormally decreases) and more dispersive phonon branches in low-frequency range, which boosts the three-phonon scattering channels (reflected by the weighted phase space) and eventually suppress the thermal conductivity of Si24. Finally, based on a simple and effective lattice chain model, we reproduce the abnormal thermal phenomenon observed in [email protected]24, and further demonstrate that the origin stems from the strong interaction between Ca and Si24 atoms. These findings shed light on a new physical mechanism for the reduction in thermal conductivity of [email protected]24, which offers a promising approach to improve the thermoelectric efficiency of Si related materials.