We studied the symmetry of the Fe 3d wave function in magnetite below the Verwey temperature T(V) with resonant soft-x-ray diffraction. Although the lattice structure of the low-temperature phase of Fe(3)O(4) is well described by the pseudo-orthorhombic Pmca with a slight monoclinic P2/c distortion, we find that the 3d wave function does not reflect the Pmca symmetry, and its distortion toward monoclinic symmetry is by far larger than that of the lattice. The result supports a scenario in which the Verwey transition involves the ordering of t(2g) orbitals with complex-number coefficients.