MicroRNAs (miRNAs) play important roles in intestinal diseases; however, the role of miRNAs during weaning stress is unknown. In our study, six jejunal small RNA libraries constructed from weaning piglets at 1, 4 and 7 d after weaning (libraries W1, W4 and W7, respectively) and from suckling piglets on the same days as the weaning piglets (libraries S1, S4 and S7, respectively) were sequenced using Solexa high-throughput sequencing technology. Overall, 260 known swine miRNAs and 317 novel candidate miRNA precursors were detected in the six libraries. The results revealed that 16 differentially expressed miRNAs were found between W1 and S1; 98 differentially expressed miRNAs were found between W4 and S4 (ssc-mir-146b had the largest difference); and 22 differentially expressed miRNAs were found between W7 and S7. Sequencing miRNA results were validated using RT-qPCR. Approximately 11,572 miRNA-mRNA interactions corresponding to 3,979 target genes were predicted. The biological analysis further describe that the differentially expressed miRNAs regulated small intestinal metabolisms, stressful responses and immune functions in piglets. Therefore, the small intestine miRNA transcriptome was significantly different between weaning and suckling piglets; the difference varied with the number of days after weaning.