Recently, the layer-by-layer (LbL) self-assembly technology has attracted the enormous interest of researchers in synthesizing various pharmaceutical dosage forms. Herewith, we designed a biocompatible drug delivery system containing the calcium carbonate microparticles (CaCO3 MPs) that coated with the alternatively charged polyelectrolytes, i.e., poly-L-ornithine (PLO)/fucoidan by LbL self-assembly process (LbL MPs). Upon coating with the polyelectrolytes, the mean particle size of MPs obtained from SEM observations increased from 1.91 to 2.03 μm, and the surface of LbL MPs was smoothened compared to naked CaCO3 MPs. In addition, the reversible zeta potential changes have confirmed the accomplishment of layer upon a layer assembly. To evaluate the efficiency of cancer therapeutics, we loaded doxorubicin (Dox) in the LbL MPs, which resulted in high (69.7%) drug encapsulation efficiency. The controlled release of Dox resulted in the significant antiproliferative efficiency in breast cancer cell line (MCF-7 cells), demonstrating the potential of applying this innovative drug delivery system in the biomedical field.