The development of n‐type organic thermoelectric materials, especially π‐conjugated small molecules, lags far behind their p‐type counterparts, due primarily to the scarcity of efficient electron‐transporting molecules and the typically low electron affinities of n‐type conjugated molecules that leads to inefficient n‐doping. Herein, the n‐doping of two functionalized (carbonyl vs dicyanovinylene) indenofluorene‐based conjugated small molecules, 2,8‐bis(5‐(2‐octyldodecyl)thien‐2‐yl)indeno[1,2‐b]fluorene‐6,12‐dione (TIFDKT) and 2,2′‐(2,8‐bis(3‐alkylthiophen‐2‐yl)indeno[1,2‐b]fluorene‐6,12‐diylidene)dimalononitrile (TIFDMT) are demonstrated, with n‐type dopant N‐DMBI. While TIFDKT shows decent miscibility with N‐DMBI, it can be hardly n‐doped owing to its insufficiently low LUMO. On the other hand, TIFDMT, despite a poorer miscibility with N‐DMBI, can be efficiently n‐doped, reaching a respectable electrical conductivity of 0.16 S cm−1. Electron paramagnetic resonance measurements confirm the efficient n‐doping of TIFDMT. Based on density functional theory (DFT) calculations, the LUMO frontier orbital energy of TIFDMT is much lower, and its wave function is more delocalized compared to TIFDKT. Additionally, the polarons are more delocalized in the n‐doped TIFDMT. Remarkably, as indicated by the grazing‐incidence wide‐angle X‐ray scattering (GIWAXS), the molecular order for TIFDMT thin‐film is enhanced by n‐doping, leading to more favorable packing with edge‐on orientation and shorter π‐π stacking distances (from 3.61 to 3.36 Å). This induces more efficient charge transport in the doped state. Upon optimization, a decent thermoelectric power factor of 0.25 µWm−1K−2 is achieved for n‐doped TIFDMT. This work reveals the effect of carbonyl vs dicyanovinylene on the n‐doping efficiency, microstructure evolution upon doping and thermoelectric performance, offering a stepping stone for the future design of efficient n‐type thermoelectric molecules.