In micro-electrical discharge machining (micro-EDM) milling, the cross-section of the microgroove machine is frequently not an ideal rectangle. For instance, there are arc shapes on the bottom and corners, and the sidewall is not steep. The theoretical explanation for this phenomenon is still lacking. In addition to the tip discharge effect, the essential reason is that there is an accumulative difference in time and space during the shape change process of a tool electrode and the microstructure formation on a workpiece. The process parameters are critical influencing factors that determine this accumulative difference. Therefore, the accumulative difference mechanism in time and space is investigated in this paper, and then a theoretical model is developed to simulate the micro-EDM milling process with a straight-line single path. The simulation results for a cylindrical electrode at the two rotational speeds of 0 (nonrotating) and 300 rpm are compared, while the results for a cylindrical electrode and a square electrode at a rotation speed of 0 are also compared to verify that different process parameters generate accumulative differences in the time and space of material removal. Finally, micro-EDM milling experiments are carried out to verify the simulation model. The maximum mean relative deviation between the microgroove profiles of simulation results and those of experiments is 11.09%, and the profile shapes of simulations and experiments have a good consistency. A comparative experiment between a cylindrical electrode and a hollow electrode is also performed, which further verifies the mechanism revealed in the study. Furthermore, the cross-section profile of a microgroove can be effectively controlled by adjusting the process parameters when utilising these accumulative differences through fabricating a microgroove with a V-shaped cross-section by a square electrode and a microgroove with a semi-circular cross-section by a cylindrical electrode. This research provides theoretical guidance for solving the problems of the machining accuracy of detail features in micro-EDM milling, for instance, to machine a microgroove with an ideal rectangular cross-section.