Hydrogel microcapsules are improved transplantation delivery vehicles for pharmaceuticals by effectively segregating the active ingredients from the surroundings and delivering them to a certain target site. Layer-by-layer (LbL) assembly is an attractive process to fabricate the nano-sized hydrogel microcapsules. In this study, nano-sized hydrogel microcapsules were prepared through LbL assembly using calcium carbonate nanoparticles (CaCO3 NPs) as the sacrificial inorganic template, sodium alginate (SA) and polyethyleneimine (PEI) as the shell materials. Ciprofloxacin was used to study the encapsulation and release properties of the hydrogel microcapsules. The hydrogel microcapsules were further adsorbed onto the paper to render antimicrobial properties. The results showed that the mean size of the CaCO3 template was reduced after dispersing into sodium n-dodecyl sulfate (SDS) solution under sonication. Transmission electron microscope (TEM) and atomic force microscope (AFM) revealed that some hydrogel microcapsules had a diameter under 200 nm, typical creases and collapses were found on the surface. The nano-sized PEI/SA hydrogel microcapsules showed high loading capacity of ciprofloxacin and a sustained release. PEI/SA hydrogel microcapsules rendered good antimicrobial properties onto the paper by the adsorption of hydrogel microcapsules, however, the mechanical properties of the hygiene paper were decreased.