Craig Fagan opened the scoring from an acute angle having latched on to Jovan Kirovski's centre.
Blues doubled their lead when a Bryan Hughes free-kick was headed home by unmarked centre-back Joey Hutchinson.
Number three came on 35 minutes when Darren Carter hit a 25 yard drive past Bolton keeper Chris Stringer.
Tresor Luntala had a good shot from 20 yards out that just cleared the crossbar.
Wednesday showed a bit more fight after the interval and Ian Bennett saved a header by Matthew Shaw who connected with a cross by former Blues on-loan defender Ian Hendon.
Carter, suffering from a groin strain, was replaced by Sam Alsop on 53 minutes.
Blues: Bennett, Luntala, Hutchinson, Hipkiss, Capaldi, Carter, Hughes, Grondin, Kirovski, Fagan, Horsfield. Subs: Davies, Luckett, Courtney, Alsop, Barrowman
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