Time synchronisation has been extensively used in wireless sensor networks in many contexts, such as data fusion, TDMA schedules and synchronised sleep periods. Precision is the basic requirement for time synchronisation in wireless sensor networks. Existing time synchronisation methods were not designed to deal with dynamic environment changes. In this paper, we propose an error compensation algorithm which is designed to compensate errors caused by hardware clock drift and environment changes. The algorithm works according to a level hierarchy: the nodes in each level have the same hop and linear regression is adopted to analyse clock drift. The compensation mechanism decreases the instability caused by crystal oscillators and eliminates errors accumulated during running time. The algorithm is implemented on the SIA2420 platform using TinyOS and the results show the reliability of our algorithm.