The contradiction of near‐infrared II (NIR‐II) emission and photothermal effects limits the development of phototheranostic agents (PTAs) in many emerging cutting‐edge applications. Organic aggregates present a promising opportunity for the balance of competitive relaxation processes through the manipulation of molecular structure and packing. Herein, side chain phenyl isomerization‐induced spatial conjugation was proposed for constructing A‐D‐A type NIR‐II PTAs with simultaneous enhancement of fluorescence brightness and photothermal properties. Three pairs of mutually isomeric fluorophores, whose phenyls respectively located at the outside (o‐series) and inside (i‐series) of the side chain, were designed and synthesized. The positional isomerization of the phenyl endows the o‐series crystals with strong spatial conjugation between the phenyl group on the side chain and the backbone, as well as interlocked planar network, which is different to that observed in the i‐series. Thus, all o‐series nanoparticles (NPs) exhibit red‐shifted absorption, enhanced NIR‐II emission, and superior photothermal properties than their i‐series counterparts. A prominent member of the o‐series, o‐ITNP NPs, demonstrated efficacy in facilitating NIR‐II angiography, tumor localization, and NIR‐II imaging‐guided tumor photothermal therapy. The success of this side chain phenyl isomerization strategy paves the way for precise control of the aggregation behavior and for further development of efficient NIR‐II PTAs.