The blisk is a core component of an aero-engine, and electrochemical machining (ECM) is the primary method for its manufacture. Among several ECM methods for blisks, multi-tool synchronous machining is the most efficient and advantageous for machining channels. The allowance distribution of the blank after blisk channel machining directly influences the blade profile accuracy. This paper proposes a trajectory control strategy to homogenize the allowance distribution of the blisk channel in multi-tool ECM. The strategy includes the design of the three-dimensional space motion of the tool and blisk, as well as the regulated feed speed. The structural characteristics of the blisk channel and the principle of ECM allow for designing and optimizing the multi-dimensional trajectory. The electric field simulations elucidate the influence law of the three-axis feed speed on the side gap. An algorithm is adopted to iteratively optimize the speeds for different positions to realize multi-dimensional motion control and allowance homogenization. The proposed trajectory control strategy is applied to ECM experiments for the blisk channel. Compared with the constant feed speed mode, the regulated speed strategy reduces the maximum allowance difference between the convex (CV) profiles by 36.18% and that between the concave (CC) profiles by 37.73%. Subsequently, the one-time ECM of eight blisk channels was successfully realized. The average time for a single channel was 12.5 min, significantly improving the machining efficiency. In conclusion, the proposed method is effective and can be extended for synchronously machining various blisk types with twisted channels.