It strengthens their place in the promotion play-off positions as they chase a quick return to the Championship.
Leading marksman Gary Hooper paved the way with a goal in each half.
He opened the scoring after 36 minutes taking the ball round goalkeeper Mark Cousins before finding the net with a good finish.
He struck again after 59 minutes when a quickly taken throw-in sent him racing clear from the halfway line to beat Cousins with an excellent finish for his 29th goal of the season.
But it was not all one-way traffic with Colchester looking dangerous in the early stages.
Twice winger Mark Yeates opened up the Scunthorpe defence only to hold his head in frustration when there was no-one in the box to finish off his good work.
It was Yeates who was involved in a controversial incident early in the second half when he went down in the box under a challenge from full-back Andrew Wright but there was no penalty.
The visitors were also out of luck when striker Karl Hawley unleashed a terrific dipping shot from the edge of the box which beat goalkeeper Joe Murphy only to come back into play after hitting both the bar and a post.
It was Scunthorpe who made certain of the points when they struck again in the 69th minute with a brilliant finish from teenage midfield man Henri Lansbury, on loan from Arsenal.
He drilled a shot into the bottom corner past Cousins for his third goal for the club.
As frustration built up in the closing stages for Colchester there was a booking for Yeates as they suffered what was only their sixth away defeat of the season.