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We predict an allotrope of yttrium with an incommensurate host-guest structure by using ab initio random structure searching technique, based on first-principles calculation. Along with this, we propose a set of analogous commensurate supercells, which is an incommensurate ratio (c(H)/c(G)), by approximating the different the number of guest atoms in channels in along c axis of the host structure. Herein, our results show that c(H)/c(G) = 5/4 is energetically stable. Subsequently, the incommensurate host-guest structure is found to be thermodynamically and dynamically stable within harmonic level. The hybridization of spd explains the stability of the host-guest structure under high pressure conditions. The distributions of electrons between the host and guest atoms indicate the strong and weak electron localizations of spd bonds. This findings suggest that the host-guest structure is more likely to be achieved experimentally in this metallic element at moderate pressure.