The removal and control of inclusions has always been a hot issue in the field of metallurgy, and rare earth modifying is a proven method. However, some rare earth inclusions cannot be accurately judged due to the necessary assumptions for thermodynamic calculations and the lack of certain thermodynamic data. On the other hand, most of the currently reported researches focus on the changes in the morphology of the inclusions, and rarely involve the inherent properties of the inclusions. To address these two deficiencies, this work investigated elaborately the stability, elastic modulus, elastic anisotropy and thermal expansion coefficient of yttrium (Y) inclusions in micro alloyed steels by first-principles calculation. Then, the role of yttrium inclusion in the initial stage of crack initiation was discussed. The results showed that it was practical to judge the possibility of unknown inclusions formation in steel by formation enthalpy. The inclusions were changed from Al2O3 to Y2O3, Y2O2S, YAlO3-Y2Si2O7 composite inclusions with yttrium treatment, which was consistent with the metallographic observations. The bulk modulus (B), shear modulus (G), Young’s modulus (E), and Poisson’s ratio (σ) were calculated in a framework of the Voigte-Reusse-Hill approximation. In light of B/G and σ values, Al2O3 showed apparent brittleness, and the toughness of yttrium inclusions were improved to varying degrees compared to Al2O3 inclusions. Moreover, the order of the degree of elastic anisotropy for these inclusions was Y2Si2O7 > Al2O3 > Y2O3 > Y2O2S > YAlO3. Furthermore, the thermal expansion coefficient of Y2O3, Y2O2S, YAlO3 inclusions at any temperature were greater than that of Al2O3 and were relatively close to that of Fe, whereas, Y2Si2O7 inclusion was much larger than that of Fe. Finally, the difference between yttrium inclusions and iron matrix in the aspect of incompressibility, brittleness, toughness, mechanical anisotropy, and thermal expansion was reduced significantly, thereby improving the consistency of the matrix, this could be used to explain the phenomenon of alleviating stresses concentration and delaying the formation of micro voids.