Scope Human milk exosomes provide a natural means of genetic material transfer to infants; however, the effect of gastric/pancreatic digestion milk exosomes stability and their microRNA content is largely unknown. Methods and results We took a simulated gastric/pancreatic digestion protocol to perform in vitro digestion of milk exosomes, explore intestinal epithelial uptake, and further elucidate microRNA responses to digestion at early‐, mid‐, late lactation by massive parallel sequencing. Both undigested and digested exosomes enter human intestinal crypt‐like cells (HIEC), with evidence of nuclear localization. We identified 288 mature microRNAs from all 24 exosome samples, and an additional 610 at low abundance. A large number of synapse development‐ and immune‐related microRNAs were identified. hsa‐miR‐22‐3p was the most abundant microRNA, and the top 15 microRNAs contributed ∼11% of the sequencing reads. Upon digestion, the overall microRNA abundance in human milk exosomes was stable. Conclusion Our results for the first time reveal the survivability and complexity of human milk exosome microRNAs upon simulated gastric/pancreatic digestion, and the dynamics during lactation stages. The results suggest a previously underexplored area of infant response to genetic material in human milk exosomes. After simulated gastric/pancreatic digestion mimicking human infant gut environment, human milk exosomes are taken up by crypt‐like HIEC cells, with evidence of nuclear localization. Two hundred and eighty eight mature exosome microRNAs from 24 milk samples collected at different lactation stages, and an additional 610 at low abundance. A large number of synapse development‐ and immune‐related microRNAs were identified. Upon digestion, the overall microRNA abundance in human milk exosomes was stable.