Abstract: In the case of hydrogen masers and cesium clocks joint time-keeping without an external tracing link, to solve the problem that the weighted average algorithm can’t give full play to the long-term stability of the cesium clocks due to the small weight assigned to the cesium clocks by the occasions that focus on shortterm stability, a two-stage Kalman filter algorithm to generate local atomic timescale is proposed in this paper. The first-stage Kalman filter uses the cesium clock to calculate the frequency drift of the hydrogen masers and calibrates the frequency drift of the hydrogen masers. The second-stage Kalman filter uses a single-state variable model to generate the local atomic time which is based on the data of cesium clocks and hydrogen masers whose drift has been calibrated. The experimental results show that the longterm stability of the local atomic timescale can be improved on the premise of maintaining short-term stability: the improvement of 10-day-stability is in 10^-15 and the improvement of month-stability is in 10^-14. It is shown that the long-term stability of the local atomic timescale generated by the proposed algorithm is better.