We study the torus equivariant Schubert classes of the Grassmannian of non-maximal isotropic subspaces in a symplectic vector space. We prove a formula that expresses each of those classes as a sum of multi Schur-Pfaffians, whose entries are equivariantly modified special Schubert classes. Our result gives a proof to Wilson's conjectural formula, which generalizes the Giambelli formula for the ordinary cohomology proved by Buch-Kresch-Tamvakis, given in terms of Young's raising operators. Furthermore we show that the formula extends to a certain family of Schubert classes of the symplectic partial isotropic flag varieties.