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Ultrafast time‐domain thermoreflectance (TDTR) is utilized to extract the through‐plane thermal conductivity (Λ_LSCO) of epitaxial La_0.5Sr_0.5CoO_3−δ(LSCO) of varying thickness (<20 nm) on LaAlO₃and SrTiO₃substrates. These LSCO films possess ordered oxygen vacancies as the primary means of lattice mismatch accommodation with the substrate, which induces compressive/tensile strain and thus controls the orientation of the oxygen vacancy ordering (OVO). TDTR results demonstrate that the room‐temperatureΛ_LSCOof LSCO on both substrates (1.7 W m⁻¹K⁻¹) are nearly a factor of four lower than that of bulk single‐crystal LSCO (6.2 W m⁻¹K⁻¹). Remarkably, this approaches the lower limit of amorphous oxides (e.g., 1.3 W m⁻¹K⁻¹for glass), with no dependence on the OVO orientation. Through theoretical simulations, origins of the glass‐like thermal conductivity of LSCO are revealed as a combined effect resulting from oxygen vacancies (the dominant factor), Sr substitution, size effects, and the weak electron/phonon coupling within the LSCO film. The absence of OVO dependence in the measuredΛ_LSCOis rationalized by two main effects: (1) the nearly isotropic phononic thermal conductivity resulting from the imperfect OVO planes when δ is small; (2) the missing electronic contribution toΛ_LSCOalong the through‐plane direction for these ultrathin LSCO films on insulating substrates.