In this paper, the mode-locked pulse generation and annihilation dynamics in ultrafast fiber lasers based on pump intensity modulation are investigated by using real-time Fourier transform spectral probing. The results show that the laser outputs stable mode-locked pulses when the pump modulation voltage is at a high level. As the modulation voltage jumps to a low level, the intensity of the mode-locked pulse decreases, and then undergoes a period of decaying oscillation before annihilation occurs, and after ~5 μs the soliton is reconstructed from the noise, accompanied by the generation of the Q-modulation instability. In the low-level phase, the annihilation process in the laser cavity occurs continuously with a period of ~55 μs. By changing the duty cycle of the modulation pump, it is possible to control the the number of times solitons continuously annihilate under low-level modulation. Further, the continuous switching process of mode-locking and soliton annihilation is related to the modulation frequency of the pump, and the increase of the modulation frequency can effectively shorten the duration of the two states, thus reducing the number of soliton annihilations. In addition, by reducing the value of the low level, the gain in the laser cavity can be reduced, resulting in a shorter period of successive soliton annihilation. The results of the study are conducive to an in-depth understanding of the formation and annihilation dynamics of solitons, and provide new perspectives for developing various operation mechanisms of ultrafast lasers.