For Wireless Sensor Network (WSN), many applications rely on the coordination of synchronized clock nodes. However, the crystal oscillator of the node is affected by itself and the external environment, so that the clock skew and clock offset change and then lead to the clocks falling out of synchronization. Consequently, a new clock synchronization algorithm based on distributed Kalman filter and consistency compensation, namely DKFCC, was proposed. First of all, the optimal estimation of the clock skew and offset was obtained by two-way message exchange mechanism and distributed Kalman filter. Then consistency compensation method based on the optimal estimation value of clock parameters was adopted to achieve clock synchronization. The experimental results show that compared with the Asynchronous Consensus-based time synchronization (AC) algorithm in the WSN with 100 randomly-deployed nodes, the Synchronous Root Mean Square Error (SRAMSE) of the DKFCC synchronization algorithm with virtual global consistency is reduced by about 95%, which means DKFCC synchronization algorithm has higher synchronization accuracy. At the same time, the proposed algorithm achieves synchronization from the clock parameter level without operating clock synchronization frequently, thus it has better energy efficiency compared to AC synchronization algorithm.