Soliton molecules in mode-locked lasers are expected to be ideal self-organization patterns, which warrant stability and robustness against perturbations. However, recent ultra-high resolution optical cross-correlation measurements uncover an intra-molecular timing jitter, even in stationary soliton molecules. In this work, we found that the intra-molecular timing jitter has a quantum origin. Numerical simulation indicates that amplified spontaneous emission (ASE) noise induces a random quantum diffusion for soliton pulse timing, which cannot be compensated by soliton binding mechanism. By suppressing indirectly coupled timing jitter at close-to-zero cavity dispersion, a record-low 350 as rms intra-soliton-molecular jittering is obtained from an Er-fiber laser in experiment. This work provides insight into the fundamental limits for the instability of multi-soliton patterns.