Increasing environmental concern has put forward the use of flax fibers instead of glass fibers in composite materials. However, durability performances of these bio-fibers remain one of their main issues. This study focuses on the hydrothermal aging of flax fibers. Flax tows were immersed in distilled water at a temperature of 80 °C for different durations. The effect of the hydrothermal aging on mechanical properties of flax tows was evaluated. Results showed a strong decrease in the maximal strength and the stiffness by 31% and 49%, respectively, until one week of aging. Multi-scale analyses were realized to explain these evolutions. Morphological characterization highlighted a washing of fiber surfaces during the hydrothermal aging, extracting amorphous components as pectins, lignins and amorphous hemicelluloses from cortical tissues. We showed that this morphological evolution impacted the fiber crystallinity. Based on a mechanical analysis, we showed that amorphous components extraction may be at the origin of the material softening. Moreover, the amorphous phase in particular the natural binder pectin would play a major role in the fiber stiffness but does not modify the flaws at the origin of failure.