Objective To investigate the in vitro and in vivo release of chitosan-alginate microgels coated layer-by-layer by polyelectrolyte self-assembly. Methods The cores of the microgels were made by gelatinization using electrostatic microencapsulated and coated by polyelectrolytes using electrostatic attraction.The effects of different layers and ratios of polymer on the in vitro release of FITC-dextran were evaluated. Histological examination was carried out to observe the in vivo release process by injecting the coated microgels into mice. Results The results showed that alginate and calcium chloride concentrations and polyelectrolyte layers markedly affected the lag time of pulsed release and the releasing speed after lagging. Conclusion The release of microgels coated layer-by-layer by polyelectrolyte can be controlled in vitro and can be observed in vivo; meanwhile, the microgels are safe and have good biocompatibility.