Cross-adaptation, which can improve the stress tolerance of strains, temporarily supplies more matching bases in transcriptome-phenotype matching approaches to reveal novel gene functions in stress responses. Transcriptome-phenotype matching based on RNA sequencing was implemented to reveal the cross-adaptation mechanism of Lactobacillus rhamnosus hsryfm 1301 in response to heat stress and oxidative stress. A total of 242 genes were upregulated and 320 genes were downregulated under heat stress, while 135 genes were upregulated and 206 genes were downregulated under oxidative stress. There were 154 overlapping genes that responded to both stresses, and 97.4% of the overlapping DEGs (differentially expressed genes) were codirectionally regulated. The overlapping DEGs were mainly classified into amino acid or oligopeptide ABC transporters, amino acid metabolism, and quorum sensing pathways. Correspondingly, the heat and oxidative tolerance of L. rhamnosus hsryfm 1301 was stronger in low nitrogen source environment. Thus, the high proportion of transcriptional homogenization, especially the decrease in abundance of nitrogen source transporter and metabolism enzyme genes, was a reason for the cross-adaptation of L. rhamnosus hsryfm 1301 to heat stress and oxidative stress. The survival rate of L. rhamnosus during processes with heat stress and oxidative stress can be improved by reducing the concentration of nitrogen source in the culture medium.