Lipids significantly affect embryo cryopreservation in some mammalian species depending on the cell lipidome quantity and composition. One of the ways to study the relationship between lipid content and cryotolerance of cells is to study the effect of lipidome modification on laboratory mice. The objective of this research was to study how in vitro culture of mouse embryos with linoleic acid (LA) will affect lipid phase transition (LPT) during cooling and subsequent embryo development after cryopreservation. Embryos obtained in vivo at the 2-cell stage were cultured with 200 μM LA for 46 h up to the morula/blastocyst stage. Thereafter, one portion of embryos was slowly frozen to reveal the effect of LA on survival after cryopreservation, another portion was used to characterize the lipid composition and to determine the temperature of the LPT onset. Confocal fluorescence microscopy of Nile Red stained embryos showed a significant increase in lipid content of the LA treated group compared to the controls. Raman measurements showed that the onset of LPT in LA treated embryos is lower than in untreated ones: −5 °C vs +2 °C. However, these changes in the LPT onset did not affect the survival rates of embryos after cryopreservation. In summary, in vitro culture with LA changes the biophysical characteristics of embryos’ lipidome and is realized in lower LPT onset, but this does not affect embryo survival after cryopreservation.