A novel annulation protocol has been successfully developed in this work for the quick generation of 1,3,4,6,11,11a-hexahydro-2H-pyrazino[1,2-b]isoquinolines from easily accessible o-alkynylbenzaldehydes. Various hexahydropyrazinoisoquinolines, including those previously unavailable with electron-deficient substituents, have been achieved via the newly developed continuously operational isochromenylium/isoquinolinium-mediated procedure. It also perfectly served as a key step to generate the basic skeleton in the new total synthesis of quinocarcinol, accompanied by the development and application of a direct late-stage stereoselective sp3 C-H hydroxymethylation.