Micro electrochemical machining (ECM) has the advantages of non-contact machining, no tool loss and no residual stress, and has great development potential in the field of microstructure manufacturing. However, the micron-scale machining gap is difficult to renew and discharge the electrolyte and electrolytic products in time. In this paper, a novel micro ECM with programmable dynamic eccentric rotating electrode (DER-ECM) is proposed, which can effectively improve the discharge of electrolytic products in the machining area. According to the process characteristics, a disc flexure hinge structure with one-stage amplification was designed, which was driven by a piezo-ceramic actuator, and the programmable eccentricity ranging from 0 to 20 μm. The multi-physics model of flow field and electric field of DER-ECM, micro ECM with eccentric rotating electrode (ER-ECM) and micro ECM with rotating electrode (R-ECM) were established. The theoretical simulation results showed that the flow rate generated by DER-ECM at the bottom of the electrode is 97 times that of ER-ECM. The current density generated by DER-ECM showed periodic pulsation, and the pulsation period was determined by the driving frequency of the piezo-ceramic actuator. The experimental results showed that DER-ECM could effectively eliminate the surface spike of the workpiece in the bottom machining area and effectively improve the machining accuracy. The micro-groove widths obtained under DER-ECM, ER-ECM and R-ECM were 418 μm, 446 μm and 468 μm, respectively. In addition, the influence of three types of dynamic eccentric rotation electrode trajectories on DER-ECM was studied. The experimental results showed that the sawtooth dynamic eccentric rotation electrode had better machining accuracy. Theoretical simulation and experimental results showed that DER-ECM could improve the flow field and achieve higher machining efficiency and machining localization.