Antifreeze peptides can protect cell membranes and maintain the cell viability of probiotics under cold stress. Given this, antifreeze peptides were prepared from tilapia processing byproducts of tilapia skin by enzymolysis using the response surface methodology (RSM) method. The cryoprotective effects on Lacticaseibacillus rhamnosus ATCC7469 were investigated. Trypsin was selected as the protease for tilapia skin hydrolysis. The optimal hydrolysis conditions consisted of the amount of enzyme (2200 U/g), solid–liquid ratio (1:10, w/v), reaction temperature (49 °C), and reaction time (6.8 h), and the relative survival rate of L. rhamnosus reached 98.32%. Molecular weight (Mw) distribution and peptide sequences of the antifreeze peptides prepared from tilapia skin (APT) under the optimal conditions were analyzed. APT significantly reduced the leakage of extracellular proteins and protected β-galactosidase and lactate dehydrogenase activities of L. rhamnosus. Compared with the saline group, scanning electron microscopy (SEM) observation showed that cells had a more normal, smooth, and entire surface under the protection of APT. These findings indicate that APT can be a new cryoprotectant in preserving probiotics.