Flow-based　microfluidic　biochips　are　one　of　the　most　promising　platforms　used　in　biochemical　and　pharmaceutical　laboratories　due　to　their　high　efficiency　and　low　costs.　Inside　such　a　chip,　fluids　of　nanoliter　volumes　are　transported　between　devices　for　various　operations,　such　as　mixing　and　detection.　The　transportation　channels　and　corresponding　operation　devices　are　controlled　by　microvalves　driven　by　external　pressure　sources.　Since　assigning　an　independent　pressure　source　to　every　microvalve　would　be　impractical　due　to　high　costs　and　limited　system　dimensions,　states　of　microvalves　are　switched　by　a　control　logic　using　time　multiplexing.　Existing　control-logic　designs,　however,　still　switch　only　a　single　control　channel　per　operation,　leading　to　a　low　efficiency.　In　this　article,　we　present　the　first　automatic　synthesis　approach　for　a　control　logic　that　is　able　to　switch　multiple　control　channels　simultaneously.　Moreover,　we　propose　the　first　fault-aware　design　in　control　logic　by　introducing　backup　control　paths　to　maintain　the　correct　function　even　when　manufacturing　defects　occur.　The　construction　of　control　logic　is　achieved　by　a　highly　efficient　framework　based　on　particle　swarm　optimization,　Boolean　logic　simplification,　grid　routing,　together　with　mixing　multiplexing.　The　simulation　results　demonstrate　that　the　proposed　multichannel　switching　mechanism　leads　to　fewer　valve-switching　times　and　lower　total　logic　cost,　while　realizing　fault　tolerance　for　all　control　channels.