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Co-microencapsulation technique is a common method to increase the efficiency of probiotics during the process as well as their controlled and targeted release in the gastrointestinal tract. Thus, in the current research, to improve the viability of microorganisms in harsh gastrointestinal condition, the probiotic bacteria Lactobacillus rhamnosus was encapsulated in sodium alginate and pectin (as co-microencapsulating wall materials) using extrusion technique and then freeze-dried. Then the samples were placed in simulated conditions of stomach (pepsin enzyme, pH = 1.8) and small intestine (bile salt (bile oxalate) and pancreatin enzyme, pH = 6.8) for a total of 5 hours. Samples of optimal (co-microcapsule) and control (free cell and microcapsule) were characterized to investigation of physicochemical properties using FE-SEM, XRD and FT-IR assay. According to obtained results, the survival rate of free cells reduced to 62.52% after the passage through the gastrointestinal tract, while the viability of co-microcapsules and microcapsules reached 83.49% and 74.83%, respectively. Therefore, it is worth mentioning that the performance of co-microencapsulated probiotics was much higher than the acceptable level, due to the synergistic effect of the bioactive substances used. In summary, this study demonstrated that the co-microencapsulation network could be employed as a new system in the preservation of probiotics in the functional food industry.