MicroRNAs (miRNAs) play important roles in various aspects of plant physiology and metabolism. The expression level of miR164c is negatively correlated with seed vigor in rice (Oryza sativa L.); however, the mechanism of seed vigor regulation by miR164c remains unknown. Here, we studied the proteomic difference between seeds of the wild-type rice cultivar ‘Kasalath’ and its transgenic derivatives, miR164c-silenced line (MIM164c) and miR164c overexpression line (OE164c), with significant differences in anti-aging capacity. We hope that it can provide new insights into the mechanism of miRNA on regulating seed vigor.