Small-sized inner intersecting holes are a common structure for large engine nozzles, hydraulic valves, and other parts. In order to ensure the uniform and stable fluid state in the intersecting hole, it is necessary to process the fillet at the intersecting line and accurately control the fillet radius. Limited by the structure and size, the rounding of the small-sized inner intersecting hole is a technical problem, and the traditional machining methods have problems, in terms of efficiency and accuracy. In order to solve this problem, electrochemical machining technology was applied to the rounding of small-sized inner intersecting holes. According to the structure of inner intersecting holes, an electrochemical rounding processing scheme with built-in fixed cathode was designed. The electric field distribution of different cathode shapes was analyzed using finite element method software. The influence of processing voltage and processing time on the current density distribution was studied for different cathode shapes, to determine the most reasonable cathode shape. Taking the inner intersecting hole with a diameter of 2 mm as the research object, and according to the analysis of the influence of processing voltage on the processing effect, a suitable control factor for controlling the rounding was processing time, and the optimal processing voltage was obtained. The formulas of fillet radius and processing time were obtained by regression analysis and verified using machining examples. The results provide a feasible method for the accurate and controllable machining of small-sized inner intersecting hole rounding.