This article is devoted to the further development of a viable technology for low-temperature cryopreservation of reproductive cells of sturgeon fish using acoustic–mechanical fields and intelligent control of the freezing process. Before vitrification begins, the piezoactuator acts on a mixture of cryoprotectant and reproductive cells. This promotes intensive mixing of the cryoprotector and its diffusion through the cell membrane. When vitrification is carried out directly, a phase transition phenomenon is observed, accompanied by crystal formation. This article presents a new mathematical model describing this process as developed by the authors. The corresponding boundary conditions are formulated. Numerical experiments were carried out using the finite element method. It has been established that during vitrification without the use of a cryoprotectant, a sharp temperature jump is observed at the front of the crystalline formation boundary. The use of a cryoprotectant leads to a slowdown in the process of crystal formation, that is, to a weakening of the effect of one of the most important cryoprotective factors. The comparison with full-scale experiments showed qualitative agreement with the experimental results, which indicates the adequacy of the proposed model. The results obtained can be used in the future during the vitrification process and the evaluation of the quality of cryofreezing. The application of a new methodological approach to methods of long-term preservation at low temperatures of the genetic and reproductive material of hydrobionts using acoustic and mechanical effects and an intelligent control module opens up great opportunities for the creation of new cost-effective biotechnologies that make it possible to make the transition to a new type of aquatic farms, increase the stability of aquaculture, in general, to make environmental protection measures to save rare and endangered species more effective.