In this paper, we generalize the Lyndon-Shirshov words to Lyndon-Shirshov Ω-words on a set X and prove that the set of all non-associative Lyndon-Shirshov Ω-words forms a linear basis of the free Lie Ω-algebra on the set X. From this, we establish Gröbner-Shirshov bases theory for Lie Ω-algebras. As applications, we give Gröbner-Shirshov bases for free λ-Rota-Baxter Lie algebras, free modified λ-Rota-Baxter Lie algebras and free Nijenhuis Lie algebras and then linear bases of such three free algebras are obtained.