MicroRNAs (miRNAs) are an emerging class of small RNAs regulating a wide range of biological processes. Soybean cotyledons evolved as sink tissues to synthesize and store seed reserves which directly affect soybean seed yield and quality. However, little is known about miRNAs and their regulatory networks in soybean cotyledons. We sequenced 292 million small RNA reads expressed in soybean cotyledons, and discovered 130 novel miRNA genes and 72 novel miRNA families. The cotyledon miRNAs arose at various stages of land plant evolution. Evolutionary analysis of the miRNA genes in duplicated genome segments from the recent Glycine whole genome duplication revealed that the majority of novel soybean cotyledon miRNAs were young, and likely arose after the duplication event 13 million years ago. We revealed the evolutionary pathway of a soybean cotyledon miRNA family (soy-miR15/49) that evolved from a neutral invertase gene through an inverted duplication and a series of DNA amplification and deletion events. A total of 304 miRNA genes were expressed in soybean cotyledons. The miRNAs were predicted to target 1910 genes, and form complex miRNA networks regulating a wide range of biological pathways in cotyledons. The comprehensive characterization of the miRNAs and their underlying regulatory networks at gene, pathway and system levels provides a foundation for further studies of miRNAs in cotyledons.