In this paper, we present a configurable electrophoretic display (EPD) controller which provides a new architecture design of compacted waveform lookup tables. Compared with traditional designs of waveform LUT, the proposed method drastically shrinks the required memory size of LUTs. To improve visual quality, the controller also supports partial image update and integrates a real-time halftoning engine. The controller design has been implemented on an FPGA and successfully tested on several flexible EPDs.