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The Clique Partitioning Problem (CPP) is essential in graph theory with a number of important applications. Due to its NP-hardness, efficient algorithms for solving this problem are very crucial for practical purposes, and simulated annealing is proved to be effective in state-of-the-art CPP algorithms. However, to make simulated annealing more efficient to solve large-scale CPPs, in this paper, we propose a new iterated simulated annealing algorithm. Several methods are proposed in our algorithm to improve simulated annealing. First, a new configuration checking strategy based on timestamp is presented and incorporated into simulated annealing to avoid search cycles. Afterwards, to enhance the local search ability of simulated annealing and speed up convergence, we combine our simulated annealing with a descent search method to solve the CPP. This method further improves solutions found by simulated annealing, and thus compensates for the local search effect. To further accelerate the convergence speed, we introduce a shrinking factor to decline initial temperature and then propose an iterated local search algorithm based on simulated annealing. Additionally, a restart strategy is adopted when the search procedure converges. Extensive experiments on benchmark instances of the CPP were carried out, and the results suggest that the proposed simulated annealing algorithm outperforms all the existing heuristic algorithms, including five state-of-the-art algorithms. Thus the best-known solutions for 34 instances out of 94 are updated. We also conduct comparative analyses of the proposed strategies and show their effectiveness.