In this study, hybrid chitosan/halloysite nanotubes (Cs/HNTs) reinforced polylactic acid (PLA) were prepared via melt compounding and compression molding techniques. In the fabrication of PLA/Cs/HNTs hybrid biocomposites, the partial replacement of Cs with HNTs was performed at filler loading of 2.5 parts per hundred parts of polymer (php), proceeding from the highest tensile strength of PLA/Cs obtained in our previous study. Cs was partially replaced with different HNTs loadings (0.5, 1, 1.5, 2, and 2.5) php and its effects on the functional group, thermal, tensile, morphological, and water absorption properties were investigated systematically. The results revealed that the combined loading of 1 php Cs and 1.5 php HNTs hybrid fillers into PLA showed the best performance in all properties. Fourier transform infrared spectroscopy (FTIR) analysis indicated that the siloxane (SiO) group of HNTs had chemically interacted with the amine group of Cs. The thermal analysis demonstrated that partial replacement of Cs with 1.5 php HNTs improved the thermal stability of PLA/2.5Cs/0HNTs biocomposite by ~12%. Yet, the percentage of crystallinity (χc) reduced with HNTs addition due to the phase adhesion improvement. Moreover, PLA/1Cs/1.5HNTs hybrid biocomposites showed the highest tensile strength and elongation at break of 59 MPa and 2.72%, respectively. This correlated with the uniform dispersion and better interfacial adhesion between Cs/HNTs fillers in the PLA matrix, as confirmed by the field emission scanning electron microscopy (FESEM). In addition, partial replacement of Cs with HNTs exhibited a lower water absorption percentage, which suggested the advantage of hybrid fillers to reduce water uptake, and is beneficial in a wide range of applications.