This study employs real-time Fourier transform spectroscopy to investigate the pulsation dynamics of soliton molecules in a mode-locked erbium-doped fiber laser, utilizing pump intensity modulation. By manipulating the driving voltage of the pump source, we systematically observe and characterize the impact of external modulation signals on the amplitude, period, pulsation frequency, and the relative phase evolution among the pulsating soliton molecules within their spectra.The results demonstrate that, under specific conditions of pump intensity modulation, the pulsation period of soliton molecule spectra can be precisely regulated by the pump modulation frequency. Concurrently, the amplitude of soliton molecule pulsations and the evolution of relative phase among the solitons are intricately tied to the pump modulation frequency. At lower modulation frequencies, such as 1 kHz, the relative phase among the pulses within the soliton molecule exhibits a sliding-type dynamics as a function of propagation time.As the modulation frequency gradually increases, e.g., to 5 kHz, a scenario emerges where three soliton molecules are generated. Notably, both the soliton spacing and relative phase undergo synchronous adjustments influenced by the pump modulation. With further escalation of the modulation frequency, such as to 20 kHz, the relative phase evolution among the pulses within the soliton molecule gradually descends into chaos. This observation suggests the plausible existence of an inherent resonant frequency associated with pulsating soliton molecules, which has direct implications for their stability.The findings of this research hold significant relevance for advancing our comprehension of soliton molecule generation and enhancing their stability. Furthermore, they offer valuable insights into the broader domain of all-optical manipulation and applications of soliton molecules, as well as their utilization in pulse encoding within mode-locked laser systems.