Heat-induced inactivation of viable cells restricts a wide range of application of spray drying in producing dried lactic acid bacteria (LAB) products. In the present study, an effective method to enhance the stability of LAB under heat stress has been identified. This was done by enhancing the heat stability of skim milk as the carrier. Here, skim milk was supplemented with 10 mM CaCl2 and heated to 90 °C for 10 min to induce protein aggregation. Using this Ca-aggregated skim milk as carrier, the survival of five LAB strains tested was found two orders of magnitudes higher than that of an untreated milk after the heating at a rising temperature from about 25 to 70 °C within 45 s. Possible mechanisms of the protection were explored by comparing the residual viability, microstructure of the cell-contained milk, and changes of suspension particle sizes caused by heat treatment of the four carriers, i.e., untreated milk, Ca-added milk, heat-treated milk, and Ca-aggregated milk. Ca-aggregated milk induced the highest microbial heat stability among them, providing a thick and compact encapsulation around LAB cells before the heat treatment for inactivation. The viable cells could stay in a comparatively more stable extracellular environment. This work reveals potentially a new option for using milk protein aggregates as a protectant of microorganisms. A series of calcium-enriched probiotic products may be developed based on the described principles of the finding of the Ca-aggregated milk.