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.　©　2022,　Beijing　China　Science　Journal　Publishing　Co.　Ltd.　All　right　reserved.