Novikov algebras were introduced in connection with Poisson brackets of hydrodynamic type and Hamiltonian operators in the formal variational calculus. They also correspond to a class of vertex algebras. An automorphism of a Novikov algebra is a linear isomorphism ϕ satisfying ϕ(xy)=ϕ(x)ϕ(y) which keeps the algebraic structure. The set of automorphisms of a Novikov algebra is a Lie group whose Lie algebra is just the Novikov algebra's derivation algebra. The theory of automorphisms plays an important role in the study of Novikov algebras. In this paper, we study the automorphisms of Novikov algebras. We get some results on their properties and classification in low dimensions. These results are fundamental in a certain sense, and they will serve as a guide for further development. Moreover, we apply these results to classify Gel'fand-Dorfman bialgebras and Novikov-Poisson lgebras. These results also can be used to study certain phase spaces and geometric classical r-matrices.