Organic single crystals with near‐infrared (NIR) emission demonstrate their excellent optical communications from well photonic confinement and low optical waveguide loss, which are considered as competitive candidates toward advanced optoelectronics. However, the increasingly diverse and sophisticated application demands result in the complicated design of NIR devices, which is hardly realized solely by the intrinsic properties of individual crystals. Herein, a programmable assembly strategy is presented to fabricate organic heterostructures. Triphenylene (TP), pyrene (Py) and 7,7,8,8‐tetracyanoquinodimethane (TCNQ) are primary selected to prepared organic cocrystals with narrow band gap and near‐infrared emission. Importantly, the charge‐transfer alloy with tunable emission from 700 nm to 850 nm and branched heterostructures with multichannel characteristics are prepared from these organic cocrystals by following the growth kinetics process at molecular level and lattice matching principle at structural level, respectively. Theses prepared heterostructures exhibit optical logic operation capabilities, which can serve as optical modulators. This work provides new insights into the manufacturing of organic NIR heterostructures applied in advanced optoelectronics.