High-temperature spray drying and extrusion method have been used for the preparation of delivery systems. However, those methods can lead to the degradation of bioactive compounds and generally allow for the production of large particle size due to high heat treatment. The objectives of this research were to manufacture of a suitable delivery system for Lactobacillus rhamnosus GG (LGG) by using milk protein hybrid delivery system (MPHDS) and assess the survival rate of LGG during manufacture, storage, and exposure to the simulated gastrointestinal condition. MPHDS were prepared by using chymosin at a various temperature from 25 to 40°C for 10 min and holding time from 5 to 30 min at 25°C. The initial amount of LGG added in the preparation process with approximately 9.34 log cfu/mL and enumerated by pour plate counts in MRS agar incubated at 37°C for 48 h. All measurements were performed on 3 independent samples. The microparticles obtained were rather similar in shape (globular shape) and size (around 5 to 28 μm) in confocal laser scanning microscopy images and particle size analyzer. The encapsulation efficiency of different encapsulation treatments was increased significantly (P < 0.05) from 66.5% to 80.3%, respectively. The viability rate during manufacture using heat temperature at 65°C for 30 min and storage at 4°C for 7 d was 71.4% to 77.6% and 76.1% to 80.3% significantly (P < 0.05) higher compared with free probiotics. Furthermore, the survival rate after gastrointestinal juice exposure of all prepared microcapsules was more than 70% in simulated gastrointestinal juice (pH 2.0) and 72% in simulated intestinal juice (pH 7.5) compare with free probiotics. In conclusion, encapsulation of probiotics effectively protected LGG against adverse condition such as heat treatment, storage, and gastrointestinal conditions.