In this work, we study the timing instability of a scalar twin-pulse soliton molecule generated by a passively mode-locked Er-fiber laser. Subfemtosecond precision relative timing jitter characterization between the two solitons composing the molecule is enabled by the balanced optical cross-correlation (BOC) method. Jitter spectral density reveals a short-term (on the microsecond to millisecond timescale) random fluctuation of the pulse separation even in the robust stationary soliton molecules. The root-mean-square (rms) timing jitter is on the order of femtoseconds depending on the pulse separation and the mode-locking regime. The lowest rms timing jitter is 0.83 fs, which is observed in the dispersion managed mode-locking regime. Moreover, the BOC method has proved to be capable of resolving the soliton interaction dynamics in various vibrating soliton molecules.