The large-scale mission scheduling problem for multiple heterogeneous agile earth observation satellites is generally considered an extremely complex NP problem, which usually requires a large amount of computing resources to obtain the optimal solution or near-optimal solution. In order to solve the problem, the original chameleon swarm algorithm (CSA) is chosen to be modified from four aspects to improve its computational efficiency and global search ability. Specifically, the multi-population mechanism is introduced into the hunting prey of the modified chameleon swarm algorithm (MCSA), where the search strategies of three sub-populations and two different emergency response strategies are designed. The conflict elimination strategy based on heuristic rules is designed for the invalid solutions generated during the iteration process. Besides, the screening mechanism and the improved coding method are introduced into the MCSA based on the existing references. The results show that compared with the original CSA and two other existing referenced modified algorithms, the MCSA has significant advantages in both the computational efficiency and the global search ability, which verified the effectiveness of MCSA.