Real-time control systems of macro-micro manipulators commonly confront time-delay challenges to achieve high precision and synchronization performance, because macro and micro subsystems always have significant difference mainly in mechanical inertia. In this paper, a self-designed PC-based real-time controller utilized in laser on-the-fly processing is introduced as a study case of macro-micro systems. A dynamic time-delay compensation method for this case is proposed based on efficient fuzzy-model prediction and special data compression/extension algorithm. This method takes account of the practical time-delay fluctuation and has capability of adjusting the compensator adaptively rather than fixing the compensator as a constant, compared with the conventional static compensation. Experimental results show that, after applying the dynamic compensation, the process error caused by time-delay is eliminated from 1.059 mm to 0.001 mm, while the quality of synchronization appears even better than the static compensation with the error of 0.014 mm. Besides, the proposed method is computationally optimized, and the extra load of real-time kernel merely fluctuates within 3 % of the total computation performance capacity.