Purpose:　Flights　are　often　delayed　owing　to　emergencies.　This　paper　proposes　a　cooperative　slot　secondary　assignment　(CSSA)　model　based　on　a　collaborative　decision-making　(CDM)　mechanism,　and　the　operation　mode　of　flight　waves　designs　an　improved　intelligent　algorithm　to　solve　the　optimal　flight　plan　and　minimize　the　total　delay　of　passenger　time.　Design/methodology/approach:　Taking　passenger　delays,　transfer　delays　and　flight　cancellation　delays　into　account　comprehensively,　the　total　delay　time　is　minimized　as　the　objective　function.　The　model　is　verified　by　a　linear　solver　and　compared　with　the　first　come　first　service　(FCFS)　method　to　prove　the　effectiveness　of　the　method.　An　improved　adaptive　partheno-genetic　algorithm　(IAPGA)　using　hierarchical　serial　number　coding　was　designed,　combining　elite　and　roulette　strategies　to　find　pareto　solutions.　Findings:　Comparing　and　analyzing　the　experimental　results　of　various　scale　examples,　the　optimization　model　in　this　paper　is　greatly　optimized　compared　to　the　FCFS　method　in　terms　of　total　delay　time,　and　the　IAPGA　algorithm　is　better　than　the　algorithm　before　in　terms　of　solution　performance　and　solution　set　quality.　Originality/value:　Based　on　the　actual　situation,　this　paper　considers　the　operation　mode　of　flight　waves.　In　addition,　the　flight　plan　solved　by　the　model　can　be　guaranteed　in　terms　of　feasibility　and　effectiveness,　which　can　provide　airlines　with　reasonable　decision-making　opinions　when　reassigning　slot　resources.　©　2022,　Emerald　Publishing　Limited.