Topological insulators in three dimensions are characterized by a Z2-valued topological invariant, which consists of a strong index and three weak indices. In the presence of disorder, only the strong index survives. This paper studies the topological invariant in disordered three-dimensional system by viewing it as a super-cell of an infinite periodic system. As an application of this method we show that the strong index becomes non-trivial when strong enough disorder is introduced into a trivial insulator with spin-orbit coupling, realizing a strong topological Anderson insulator. We also numerically extract the gap range and determine the phase boundaries of this topological phase, which fits well with those obtained from self-consistent Born approximation (SCBA) and the transport calculations.PACS numbers: 72.25.Hg, Time reversal invariant band insulators of noninteracting electrons are basically divided into two classes: the ordinary insulator and the topological insulator [1][2][3][4]. The latter is a novel phase of quantum matter. It has an insulating bulk gap and gapless edge or surface states. These gapless states are topologically protected and are immune to non-magnetic disorder. Recently another kind of non-trivial quantum phase termed topological Anderson insulator (TAI) has been predicted to exist in two dimensions (2D) [5][6][7] and three dimensions (3D) [8], which makes the situation more interesting. In the TAI phase, remarkably, the topologically protected gapless states emerge due to disorder.For systems without disorder, the topological phases can be characterized by studying the gapless states as obtained e.g. from diagonalizing the Hamiltonian in a geometry with edges or surfaces. They can also be characterized by the topological invariants calculated from the bulk Hamiltonian, which have been well studied in recent literature [9,10]. However in the disordered systems, gapless modes alone cannot unambiguously identify the topological phases because they may be localized in space. Instead, the transport properties are usually used to find these extended topologically protected modes. Similarly we may also use the topological invariant to characterize the topological phases induced by disorder. A question naturally arises: how to calculate the topological invariant in the presence of disorder.At first glance, it is not obvious how to generalize the present methods from translation invariant band insulators to the disordered systems. Let us first recall the integer quantum Hall effect (IQHE) where the generalization to the case with disorder is well understood. The topological quantum number in IQHE, which characterizes the quantized Hall conductivity, is known as the first Chern number [also refered to as the Thouless-KohmotoNightingale-den Nijs (TKNN) integer] and is closely related to Berry's phase. In the presence of disorder, the TKNN integers defined for a clean system can be generalized. By introducing generalized periodic boundary conditions and averaging over different boundary condi...