The aim of this study is to simulate the self-organized evolution mechanism of inner innovation of large-scale construction enterprises (LSCE) under different contexts. Based on NK stochastic combinatorial optimization model with two parameters (N, K), this study proposes three modules—ambidexterity, punctuated equilibrium, and automation—to simulate the change behaviors of the inner innovation system. Furthermore, this study analyses the influence of factor correlation on inner innovation performance under discusses nine different combination situations. The research results show that (a) regardless of how the relationship strength changes, fitness increases with an increasing K value; and (b) the comparison of optimization modes show that the punctuated equilibrium mode can guarantee the long- and short-term inner innovation performance LSCE. This study therefore reveals the mutual effects of the factors in the inner innovation system in LSCE and provides an effective model for internal systems analyses in the construction industry and in other sectors.