The topology of non-Hermitian systems is drastically shaped by the non-Hermitian skin effect, which leads to the generalized bulk-boundary correspondence and non-Bloch band theory. The essential part in formulations of bulk-boundary correspondence is a general and computable definition of topological invariants. In this Letter, we introduce a construction of non-Hermitian topological invariants based directly on real-space wave functions, which provides a general and straightforward approach for determining non-Hermitian topology. As an illustration, we apply this formulation to several representative models of non-Hermitian systems, efficiently obtaining their topological invariants in the presence of non-Hermitian skin effect. Our formulation also provides a dual picture of the non-Bloch band theory based on the generalized Brillouin zone, offering a unique perspective of bulk-boundary correspondence.