Lignin fractions having different molecular weights and varied chemical structures isolated from kraft lignins of both softwood and hardwood via a sequential solvent fractionation technique were incorporated into a tunicate cellulose nanofibers (CNF)—starch mixture to prepare 100% bio-based composite films. The aim was to investigate the impact of lignin structural diversity on film performance. It was confirmed that lignin’s distribution in the films was dependent on the polarity of solvents used for fractionation (acetone > methanol > ethanol > ethyl acetate) and influenced the optical properties of the films. The –OH group content and molecular weight of lignin were positively related to film density. In general, the addition of lignin fractions led to decrease in thermal stability and increase in Young’s modulus of the composite films. The modulus of the films was found to decrease as the molecular weight of lignin increased, and a higher amount of carboxyl and phenolic –OH groups in the lignin fraction resulted in films with higher stiffness. The thermal analysis showed higher char content formation for lignin-containing films in a nitrogen atmosphere with increased molecular weight. In an oxygen atmosphere, the phenol content, saturated side chains and short chain structures of lignin had impacts on the maximum decomposition temperature of the films, confirming the relationship between the chemical structure of lignin and thermo-oxidative stability of the corresponding film. This study addresses the importance of lignin diversities on composite film performance, which could be helpful for tailoring lignin’s applications in bio-based materials based on their specific characteristics.