The effect on the two‐photon absorption of heptamethine cyanines (HMCy) upon polymethinic chain substitution is explained via measurements with a femtosecond laser and time‐dependent/density functional theory calculations. An analysis of the optical properties of several HMCy is presented, emphasizing the similarities and differences between IR780 and HITC (used as a case study of HMCy), mainly by analyzing meso‐substitution and investigating the effect of intermediate structures between both molecules. The two‐photon absorption cross‐section of HITC diluted in methanol was measured, yielding a peak of 1838 GM at 830 nm. Spectroscopic and electronic structure computational data show that the change of polymethine chain substituents significantly affects excited state S4 of the molecules, modulating their transition moment and relative energy which, together with changes in the molecular geometry, govern non‐linear absorption.