In this paper, we aim to introduce and characterize the numerical radius orthogonality of operators on a complex Hilbert space H which are bounded with respect to the seminorm induced by a positive operator A on H. Moreover, a characterization of the A-numerical radius parallelism for A-rank one operators is obtained. As applications of the results obtained, we derive some A-numerical radius inequalities of operator matrices, where A is the operator diagonal matrix whose each diagonal entry is a positive operator A on a complex Hilbert space H.