Agar-based nanocomposites at different halloysite loadings, with and without chitosan as an ingredient and modifier, were prepared by solution casting. The morphology of the nanocomposites was studied by field-emission scanning electron microscopy, and results showed that chitosan partly promoted halloysite dispersion in the nanocomposites. The synergetic effect of chitosan and halloysite on the mechanical properties, water resistance and transparency of the obtained nanocomposites was evaluated. Results indicated that with increased chitosan and/or halloysite content, the tensile strength and elongation at the break of nanocomposites increased significantly. When added 40% chitosan and 8% halloysite into agar matrix, the tensile strength and elongation at the break of agar/chitosan/halloysite composite was improved from 35.03 MPa to 14.79% to 48.29 MPa and 22.62%, respectively. With increasing chitosan content from 0 to 60%, the water-swelling degree of the obtained composites decreased from 409.8% to 34.7%. In addition, well-dispersed halloysite in the polymer matrix decreased the moisture uptake, water solubility and water-swelling degree of the composites. All the agar/chitosan/halloysite nanocomposite films showed >70% transparency in the visible-light region (400–800 nm), indicating that the light transmittance of the obtained nanocomposites was slightly affected by chitosan and halloysite.