Two approaches—fractional side‐chain truncation and complementary interactions—are employed in this study. In fractional side‐chain truncation, NDIDmap with the naphthalene diimide (NDI) group and the 3‐(dimethylamino)propyl (Dmap) chain is incorporated into P(NDI2OD‐T2), yielding various copolymers. Increasing the amount of NDIDmap in the polymer enhances π‐isotropy, which can improve charge transport. In complementary interactions, the NDIDmap group complexes with tris(pentafluorophenyl)borane (BCF) via complementary N–B interactions. Adding BCF to a naphthalenediimide‐based conjugated polymer with NDIDmap enhances the coherence length (Lc) of π‐stacking. However, the elongated Lc does not result in superior electron mobility, challenging the conventional perspective that long‐range π‐order is crucial for charge transport. For comparison, triphenylamine (TPA), which is electronically distinct from BCF, is used. TPA affects the thin‐film microstructure and charge‐transport parameters differently from BCF. Although the improvement in electron mobility is not very significant, this study demonstrates the effects of fractional side‐chain truncation and complementary interactions on the thin‐film microstructure and charge transport of naphthalenediimide‐based conjugated polymers, paving the way for further side‐chain engineering.