Abstract: To address the problem that the two phases of flow-level physical design, i.e., component placement and routing, are usually considered separately and their interaction is neglected, resulting in the degradation of design quality and biochip execution efficiency, an effective sequence-pair-based flow-level physical design algorithm for continuous-flow microfluidic biochips is proposed. Firstly, based on the sequence-pair representation method which can quickly enumerate and calculate the placement solution, the component placement solution is obtained by the discrete particle swarm optimization algorithm with higher solving efficiency to further improve the quality of the placement solution. Then, the Manhattan distance between component pairs is considered as the basis for routing order in the routing stage, and the routing is performed by the negotiation-based routing algorithm to effectively reduce the number of crossings in the flow channel. Finally, the interaction between placement and routing is considered, and the placement is adjusted according to the feedback information of routing, thus bridging the component placement and routing phases. The benchmark test set of actual biochemical application reaction and synthesis is adopted, and the flow-level physical design algorithm based on simulated annealing placement and negotiated routing is reproduced as the comparison algorithm for the experiment. The experimental results show that the proposed algorithm optimizes the number of flow path intersections by 74.94%, the chip area by 5.04%, and the total flow path length by 16.88%, resulting in a high-quality flow path physical design solution.