Large-scale mixed-integer linear programming (MILP) problems, such as those from two-stage stochastic programming, usually have a decomposable structure that can be exploited to design efficient optimization methods. Classical Benders decomposition can solve MILPs with weak linking constraints (which are decomposable when linking variables are fixed) but not strong linking constraints (which are not decomposable even when linking variables are fixed). In this paper, we first propose a new rigorous bilevel decomposition strategy for solving MILPs with strong and weak linking constraints, then extend a recently developed cross decomposition method based on this strategy. We also show how to apply the extended cross decomposition method to two-stage stochastic programming problems with conditional-value-at-risk (CVaR) constraints. In the case studies, we demonstrate the significant computational advantage of the proposed extended cross decomposition method as well as the benefit of including CVaR constraints in stochastic programming. (C) 2018 Elsevier Ltd. All rights reserved.