Article is devoted to the problem of software reliability estimation. The object of investigation is the software system with complex architecture. The complexity in this case means the distribution, multiple architectural levels, redundancy, in particular, multiversion architecture. Moreover, the software system may be developed according to the methodology of the structural or object-oriented programming. Necessity of the account of these properties while estimating the reliability parameters of a software system required the development of a universal model, which is presented in this paper. The developed algorithm allows applying this model for estimation the reliability parameters of software systems with different architectures. The modification of the model for estimation of the reliability of distributed multiversion software systems is given. Based on the proposed models and algorithm the program complex is developed. The paper presents the research of the dependence of various reliability parameters of a software system from the conditional and unconditional probability of failure of individual system components, as well as from the number of components of the software system. The results confirmed the adequacy and effectiveness of the developed model for complex software system reliability estimation.