The deformation and recovery behaviors of multilayer microcapsules were investigated after being forced to flow through a microchannel. The microchannel device with a constriction (5.7 μm in depth) in the middle was designed, and the multilayer microcapsules with different size and layer thickness (and thereby different mechanical strength) were used. Deformation in the microchannel was observed for all the capsules with a size larger than the constriction height, and its extent was mainly governed by the difference between capsule size and constriction height. The squeezed microcapsules could recover their original spherical shape when the deformation extent was smaller than 16%, whereas permanent physical deformation took place when the deformation extent was larger than 34%. The capsules filled with polyelectrolytes could greatly enhance their shape recovery ability due to the higher osmotic pressure in the capsule interior and could well maintain the preloaded low-molecular-weight dyes regardless of the squeezing.