Bunch charge uniformity controlling is very important for top-up operation of the storage ring. In order to monitor filling pattern and measure the bunch charge precisely, a PXI waveform digitizer-based data acquisition system has been developed to retrieve bunch charge information from BPM pickup signals. An effective sampling rate is extended to 400 GHz by waveform rebuilding technology, which overlays multi-turn data into single turn with real time sampling rate of 8 GHz. An on-line evaluation indicates that resolution and linearity of the charge measurement are better than 0.5% at input range of 0.5–12 nC.