Plant microRNAs (miRNA) are 21-24 nt endogenous small non-coding RNAs. They play key roles in plant development, adaptation to stresses and flexible environments through regulating the expression of their target genes post-transcriptionally. Besides, miRNAs are critical for regulating agronomic traits of important economic crops such as rice, maize and soybean, and have great potential in improving crop traits. This review focuses on research progresses of miRNAs involved in regulating important crop agronomic traits (including plant architecture, flowering, seeds development, stresses resistance, etc.) and their regulatory mechanisms. We also summarized the major research methods and strategies for taking advantage of miRNAs to improve crop traits and discussed the future prospects and problems for the application of miRNAs in crop traits improvement.