A coupled electron−nuclear dynamical study at attosecond time scale is performed on the HD + and H 2 + molecular ions under the influence of synthesized intense two-color electric fields. We have employed ω − 2ω and also, ω − 3ω two-color fields in the infrared/mid-infrared regime to study the different fragmentation processes originating from the interference of n − (n + i) (i = 1, 2) photon absorption pathways. The branching ratios corresponding to different photofragments are controlled by tuning the relative phase as well as intensity of the two-color pulses, while the effect of the initial nuclear wave function is also studied by taking an individual vibrational eigenstate or a coherent superposition of several eigenstates of HD + and H 2 + . By comprehensive analysis, the efficacy of the two different types of synthesized two-color pulses (ω − 2ω and ω − 3ω) are analyzed with respect to one-color intense pulses in terms of controlling the probability modulation and electron localization asymmetry and compared with previous theoretical calculations and experimental findings. Through the detailed investigation, we have addressed which one is the major controlling knob to have better electron localization as well as probability modulation.