Ikeda-Mihalcea-Naruse's double Schubert polynomials represent the equivariant cohomology classes of Schubert varieties in the type C flag varieties. The goal of this paper is to obtain a new tableau formula of these polynomials associated to vexillary signed permutations introduced by Anderson-Fulton. To achieve that goal, we introduce flagged factorial (Schur) $Q$-functions, combinatorially defined in terms of (flagged) marked shifted tableaux for flagged strict partitions, and prove their Schur-Pfaffian formula. As an application, we also obtain a new combinatorial formula of factorial $Q$-functions of Ivanov in which monomials bijectively correspond to flagged marked shifted tableaux.