Replacing traditional disposable, non-biodegradable plastic packaging with biodegradable plastic packaging is one of the key approaches to address the issue of “white pollution”. PBAT/PLA/inorganic filler composites are widely utilized as a biodegradable material, commonly employed in the field of packaging films. However, the poor dispersion of inorganic fillers in the polymer matrix and the limited compatibility between PBAT and PLA have led to inferior mechanical properties and elevated costs. In this work, we propose a simple and effective strategy to improve the dispersion of nano-CaCO3 in a PBAT/PLA matrix through solid-state shear- milling (S3M) technology, combined with mechanochemical modification and in situ compatibilization to enhance the compatibility between PBAT and PLA. The impact of varying milling conditions on the structure and performance of the PBAT/PLA/CaCO3 composites was investigated. During the milling process, PBAT and PLA undergo partial molecular chain fragmentation, generating more active functional groups. In the presence of the chain extender ADR during melt blending, more branched PBAT-g-PLA is formed, thereby enhancing matrix compatibility. The results indicate that the choice of milling materials significantly affects the structure and properties of the composite. The film obtained by milling only PBAT and CaCO3 exhibited the best performance, with its longitudinal tensile strength and fracture elongation reaching 22 MPa and 437%, respectively. This film holds great potential for application in the field of green packaging.