Abstract: To study the longitudinal motion characteristics of multi bunches in a storage ring, a bunch-by-bunch phase measurement system is developed at HLS-II. The system uses oscilloscope to collect BPM sum-signal directly, and take zero-crossing detection method combined with temporal difference (TD) method to extract the phase of bunch-by-bunch from BPM sum-signal. The system architecture, phase extraction method and some experimental results at HLS-II are introduced in this paper. In the experiment, through off-line analysis of the phase data of 5 ms bunch-by-bunch multi turns recorded by the system, the characteristic information of the synchrotron oscillation frequency, the longitudinal tuning value, the modes information of bunches oscillation and the growth rate of the oscillation mode are obtained. It is diagnosed that there are two strong longitudinal coupled-bunch unstable modes at HLS-II during the top-off constant-current operation, and the growth rates of the two oscillation modes are extracted. The results of bunch-by-bunch phase measurement and the analysis of longitudinal instability can provide references for machine study, longitudinal feedback system tuning and performance evaluation of high frequency RF system.