Knowledge of the effect of different organic molecules on spontaneous hydrate nucleation is crucial for understanding the formation of gas hydrates in marine reservoirs. Herein, microsecond MD simulations are conducted to investigate the spontaneous nucleation of CH4 hydrates in oceanic sediments. The simulation results indicate that hydrate nucleation is influenced by the coupling effects of organic molecules, clay surfaces and salt ions, where organic molecules alter hydrate nucleation by modulating the diffusion fluctuation of CH4 molecules via controlling the shape and size of CH4 nanobubbles. Furthermore, CH4 hydrates are primarily concentrated at a moderate distance away from the nanobubbles, with fewer hydrates located either close or at a more distant from the nanobubbles. In the region about 1.0 nm away from the nanobubbles, the hydrates become more unstable when closer to the nanobubbles, whereas hydrates have better stability when locating above 1.0 nm away from the nanobubbles. Different organic molecules exert distinct effects on spontaneous hydrate nucleation. Specifically, propanol adsorbed to the nanobubble surface kinetically promotes hydrate nucleation, exhibiting a distinct advantage over other organic molecules. These molecular insights expand the understanding of the formation of natural gas hydrate resources and help to effectively utilize this resource.