They were ahead after six minutes when leading marksman Sam Winnall turned on the edge of the six-yard box to rifle home his ninth goal of the season from a low cross from the right by Terry Hawkridge.
Scunthorpe increased their lead in the 30th minute when Torquay centre-back Anthony O'Connor headed a right-wing corner from Reuben Noble-Lazarus into his own net.
Three minutes later the visitors did have the ball in the net through a header from John Marquis, but it was ruled offside.
Torquay were then out of luck again when midfield man Nathan Craig rattled the bar with a free-kick from just outside the box and he was denied again early in the second half by a full length save from keeper Sam Slocombe.
But it was Scunthorpe who struck again to make it 3-0 in the 61st minute with a first ever senior goal for teenage substitute Hakeeb Adelakun, who broke free into the box to rifle a shot past keeper Martin Rice.
Marquis pulled one back for Torquay with a well-taken goal in the 78th minute but it was not enough to prevent a disappointing first return to Glanford Park for former Scunthorpe manager Alan Knill, whose Devon side remain deep in trouble at the foot of the table.