Self-assembly of dissipative solitons arouses versatile configurations of molecular complexes, enriching intriguing dynamics in mode-locked lasers. The ongoing studies fuel the analogy between matter physics and optical solitons, and stimulate frontier developments of ultrafast optics. However, the behaviors of multiple constituents within soliton molecules still remain challenging to be precisely unveiled, regarding both the intramolecular and intermolecular motions. Here, we introduce the concept of “soliton isomer” to elucidate the molecular dynamics of multisoliton complexes. The time-lens and time-stretch techniques assisted temporal-spectral analysis reveals the diversity of assembly patterns, reminiscent of the “isomeric molecule”. Particularly, we study the fine energy exchange during the intramolecular motions, therefore gaining insights into the degrees of freedom of isomeric dynamics beyond temporal molecular patterns. All these findings further answer the question of how far the matter-soliton analogy reaches and pave an efficient route for assisting the artificial manipulation of multisoliton structures.