Hydrate technology has significant application potential in the fields of phase-change cold storage, seawater desalination, gas separation, etc. The key factors influencing the development of hydrate technology are the reduction in the induction time and the promotion of nucleation and growth of hydrates. Micro-nano bubbles (MNBs) can significantly increase the nucleation rate of hydrates owing to their advantages of increasing the gas–liquid interface, enhancing mass transfer, and providing sites for nucleation. In this study, a visualization experimental system for in situ hydrate formation promoted by MNBs was developed. The induction time and the nucleation rate of methane hydrate under the action of MNBs, and the influence mechanism of different guest molecule bulk MNBs on the induction time of methane hydrate were studied. Furthermore, the effects of hydrate formation with injection of bulk MNBs and the reformation with dissociation solution were compared, and the mechanism of bulk MNBs on the memory effect of hydrates was analyzed. The results show that under the action of bulk MNBs (size 80–240 nm), the average induction time of hydrate nucleation is reduced by 80.9%, and the average nucleation rate is increased by 4.73 times. At the same time, by comparing the bulk MNBs of different guest molecules (CH4, N2, CO2, R134a), it was found that R134a has relatively mild phase equilibrium conditions and is easier to nucleate, which has an enhancement effect on the nucleation of methane hydrate. Finally, compared with the concentration changes of bulk MNBs in the dissociated solution, it was found that bulk MNBs play an important role in the hydrate memory effect. When the concentration of bulk MNBs in the dissociated solution decreases by 73.5%, the memory effect disappears, which quantitatively proves the mechanisms of bulk MNBs on memory effects.