Bunch charge uniformity control is very important for storage ring top-up operation. In order to monitor filling pattern and measure bunch charge precisely an PXI waveform digitizer based data acquisition system was developed to retrieve bunch charge information from BPM pickup signals. Effective sampling rate could be extended to 400GHz by waveform rebuilding technology , which folds multi turns data into single turn with real time sampling rate of 8GHz. Online evaluation shows charge resolution could be better than 0.5% for 1nC range.