The widespread attention garnered by the utilization of prebiotics for the regulation of intestinal flora has not yet extended to the exploration of edible fungi protein hydrolysates or peptides that possess potential prebiotic functions. In this study, Cordyceps militaris (C. militaris) ZA17-C4 mycelium protein hydrolysates were evaluated for their potential as prebiotics and thermo-protectors for Lactobacillus fermentum (L. fermentum) J26. The results showed that the addition of 0.5% C. militaris ZA17-C4 mycelium albumin hydrolysates and 1% glutenin hydrolysates promoted the proliferation of L. fermentum J26. Furthermore, the addition of 1% 5-10 kDa C. militaris ZA17-C4 mycelial albumin hydrolysate had a significant protective effect on L. fermentum J26 under the condition of treatment at 65 °C for 20 min. L. fermentum J26 viable counts were increased by three orders of magnitude compared to the control. Meanwhile, the addition of 1% of 5-10 kDa C. militaris ZA17-C4 mycelial albumin hydrolysate had a protective effect on the cell membrane of L. fermentum J26. Subsequently, several new peptides were identified using LC-MS/MS. These peptides may have potential probiotic thermo-protectants effects.