Natural chitin/CaCO3 (ChCC) complex derived from crab shell was modified and used to fabricate an organic/inorganic complex filler to enhance the optical and mechanical properties of polylactic acid (PLA) biocomposite. Crab shell was treated with NaOH to remove proteins and pulverized to produce ChCC microparticles having flake-like shape. The presence of CaCO3 in ChCC enhanced the hydrophobicity of the microparticles after treatment with fatty acids. The ChCC-filled PLA composite films prepared via melt extrusion displayed good optical properties without harsh discoloration (ΔE of 0.9%). In contrast, the film filled only with chitin showed high ΔE of 15% at same filler content, which is not commonly observed in biopolymer-filled biocomposites. Also, the ChCC-filled film exhibited higher mechanical properties, with an 8% increase in tensile strength compared to PLA, while the chitin-filled film showed a decreased tensile strength of 6% than PLA, which was attributed to the improved compatibility between the hydrophobic ChCC and the PLA matrix. The inexpensive preparation of ChCC and its application as a biocomposite filler is an attractive use of crab shell waste.