The doubly selective (DS) channel estimation in the large-scale multiple-input multiple-output (MIMO) systems is a challenging problem due to the large number of the channel coefficients to be estimated, which requires unaffordable and prohibitive pilot overhead. In this paper, firstly we conduct the analysis about the common sparsity of the basis expansion model (BEM) coefficients among all the BEM orders and all the transmit-receive antenna pairs. Then a novel pilot pattern is proposed, which inserts the guard pilots to deal with the inter carrier interference (ICI) under the superimposed pilot pattern. Moreover, by exploiting the common sparsity of the BEM coefficients among different BEM orders and different antennas, we propose a block distributed compressive sensing (BDCS) based DS channel estimator for the large-scale MIMO systems. Its structured sparsity leads to the reduction of the pilot overhead under the premise of guaranteeing the accuracy of the estimation. Furthermore, taking consideration of the block structure, a pilot design algorithm referred to as block discrete stochastic optimization (BDSO) is proposed. It optimizes the pilot positions by reducing the coherence among different blocks of the measurement matrix. Besides, a linear smoothing method is extended to large-scale MIMO systems to improve the accuracy of the estimation. Simulation results verify the performance gains of our proposed estimator and the pilot design algorithm compared with the existing schemes.