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To solve the problem of slow convergence using the Sage-Husa algorithm to estimate clock frequency on time synchronization in wireless sensor networks, a bimodal clock frequency estimation algorithm is proposed. The algorithm uses a threshold to determine which mode the clock frequency is. For the jump mode, the ratio-based method is adopted to track the clock frequency quickly. For the stable mode, the Sage-Husa method is used to improve the estimated accuracy. Finally the proposed algorithm is applied in the level-based wireless sensor network and simulated on NS2. Experimental results show that the proposed method has better performance than the current algorithms (the ratio-based method, the Least Square Algorithm, and so on) in precision and convergence.