For a single, intense 7 μm linearly polarized laser pulse, we found that the branching ratio for the fragmentation of ClCHO+ → Cl + HCO+, H + ClCO+, HCl++CO depended strongly on the orientation of the molecule (J. Phys. Chem. Lett. 2012, 3 2541). The present study explores the possibility of controlling the branching ratio for fragmentation by using two independent pulses with different frequencies, alignment and delay. Born‐Oppenheimer molecular dynamics simulations in the laser field were carried out with the B3LYP/6‐311G(d,p) level of theory using combinations of 3.5, 7 and 10.5 μm sine squared pulses with field strengths of 0.03 au (peak intensity of 3.15×1013 W/cm2) and lengths of 560 fs. A 3.5 μm pulse aligned with the C‐H bond and a 10.5 μm pulse perpendicular to the C‐H bond produced a larger branching ratio for HCl++CO than a comparable single 7 μm pulse. When the 10.5 μm pulse was delayed by one quarter of the pulse envelope, the branching ratio for the high energy product, (HCl++CO 73%) was a factor of three larger than the low energy product (Cl + HCO+, 25%). By contrast, when the 3.5 μm pulse was delayed by one quarter of the pulse envelope, the branching ratio was reversed (HCl++CO 38%; Cl + HCO+, 60%). Continuous wavelet analysis was used to follow the interaction of the laser with the various vibrational modes as a function of time. © 2018 Wiley Periodicals, Inc.