Lignin strengthened ionic liquids (ILs) have shown high potential to be used as high performance green lubricants. Strengthened lignin-ILs molecular interaction is an effective approach to improve their lubrication properties. The molecular interactions of ILs’ cation and anion containing different functional groups with lignin and efficiency on the lubricating properties have rarely been studied yet. In this work, a series of novel green lubricants with dissolved lignin in [Choline][Amino Acid] ([CH][AA]), [Tetramethylammonium][Glycine] ([N 1111 ][Gly]) and [Tetrabutylammonium][Glycine] ([N 4444 ][Gly]) ILs have been synthesized and their tribological properties were systematically investigated. The longer alkyl chain in cation without reciprocal H-bond interaction between ILs’ cation and anion has the positive effect on the anti-wear properties. In addition, the less steric effect and more negative natural charges of amino acid anion synergistically contribute to the stronger H-bond interaction between lignin and choline base ILs, which enhances lubrication film strength and thus resulting in the better tribological property of ILs/lignin green lubricants. Specifically, the wear volume loss of the steel disc lubricated by [N 4444 ][Gly] with the addition of 15% lignin is only 12% of the one lubricated by pure [N 4444 ][Gly]. This work presents a method to tune molecular interaction between lignin and ILs via the structural design of ILs’ cation and anion, which are revealed as the key factor that bridges the individual components and improves overall lubricating properties.