Yttrium disilicates (Y2Si2O7), well known for its complex polymorphism, are promising candidates for high-temperature structural materials and environmental barrier coatings due to their good properties in harsh environments. In this study, the crystal structure, elastic stiffness, and temperature dependence of the lattice thermal conductivity of β-, γ-, and δ-Y2Si2O7 are studied using first-principles calculations. Divergences of elastic stiffness are attributed to the different crystal structures and bonding strength of the polymorphs. Specially, the Si–O–Si bridge of δ phase bends with an angle of 158.1°, and this configuration enhances the bonding heterogeneity but weakens the bonding strength and stability. According to the prediction of lattice thermal conductivity using the Debye–Slack model, β-, γ-, and δ-Y2Si2O7 are characterized with very low thermal conductivity. In addition, the deviation of lattice thermal conductivities of Y2Si2O7 polymorphs is dominated by two vital factors, anharmonicity of phonon scattering and complexity of crystal structure. The present method could be used to investigate the specific factors dominating lattice thermal conductivity and may promisingly be generalized to search novel candidates with extremely low lattice thermal conductivity.