Molecular imaging technology, an advanced research area of imaging, can provide real-time, non-invasive image information of the target site in molecular level. The key of the molecular imaging technology is molecular probe. Aptamers are short oligonucleotides with high affinity and specificity to the target molecules. The targeting ability, stability and safety of aptamers are superior to traditional antibodies so that aptamers show prosperous usages in targeting drug delivery and disease diagnostics. Therefore, aptamers are considered to be an extremely ideal probes, which can guide quantum dots, magnetic nanoparticles and ultrasound contrast agents on the targets and realize optical, magnetic resonance, ultrasonic multimodal and multifunctional imaging. All of the advantages can further promote the application of molecular imaging in disease treatment and diagnosis. In this paper, we review recent developments in the application of aptamers as molecular probes in major branches of molecular imaging.