To mitigate the risk of structural failure in coastal engineering caused by soft marine soil creep, this study presents a coupled macroscopic and mesoscopic creep model of soft marine soil to predict long-term deformation behavior of the soil. First, the mesoscopic characteristics of soft marine soil (e.g., pore, particle, and morphological characteristics) under different external pressures were obtained using a scanning electron microscope. Then, both the mesoscopic and macroscopic characteristics of soil were quantified using directional probability entropy and then used as inputs to develop the model. The model predictions agree with the experimental data. In addition, the experimental results indicate linear negative correlations between porosity and pore ratio with stress—the relationships between the fractal dimension of pore distribution and probability entropy of particle orientation under stress are generally nonlinear. Further, results of sensitivity analysis indicate that the probability entropy of particle orientation is one of the most critical parameters governing long-term creep deformation behavior of soft marine soil.