The acidic ionic liquid supported on the magnetic mesoporous silica nanotubes (M-MSNTs/IL) was prepared as a new magnetic catalyst and fully characterized with FE-SEM, HR-TEM, EDS, TGA, BET, VSM, FT-IR, EDX, elemental mapping and XPS. The template of catalyst was magnetic aminated MWCNTs (M-MWCNTs/CONHBu), which removed through calcination process and magnetic mesoporous silica nanotubes (M-MSNTs) were obtained and functionalized using adenine based ionic liquid. The prepared catalyst was successfully applied as a new reusable heterogeneous catalyst for the one-pot three-component indeno[1,2-b]indole-9,10-dione derivatives in water at 75 °C. All of desired products were obtained in good to excellent yields (79–96 %) after relatively short reaction times. M-MSNTs/IL also exhibited a remarkable performance with TOF of 61.2 h-1 and TON of 86.7. The use of M-MSNTs/IL catalyst in the synthesis of indeno[1,2-b]indole-9,10-dione derivatives revealed several advantages including mild reaction conditions, high yield of pure products, clean reaction conditions, avoiding the production of toxic waste, chemical stability of the catalyst, low amount and reusability of catalyst. In addition, the applied nanocatalyst was recovered with an external magnet and reused 6 times without considerable reduction in its catalytic activity.