Natural gas hydrate (NGH) is the commanding height of future energy development strategies. Comprehensively revealing the mechanical behavior of NGH reservoirs is the primary guarantee to ensure safe utilization of hydrate resources. However, due to the complexity of accumulation and deposition, NGH in the enrichment area of reservoirs is usually not homogeneous. However, the impact of the NGH layered heterogeneous distribution on the mechanical properties of hydrate-bearing sediment (HBS) remains unclear. In this study, based on this geological background, several sets of triaxial shear tests were carried out, and a comprehensive analysis of mechanical properties was carried out by coupling acoustic characteristics tests. The stratification effect of sediments changes the stress−strain response curve of HBS from traditional strain hardening or strain softening to "secondary strain hardening"; this hardening phenomenon only occurs once and is not affected by the number of sediment layers. Also, an increasing sediment stratification effect would enhance the HBS strength and dilatancy. The sediment stratification effect will reduce the compressional and shear-wave velocity of the HBS. The sound velocity increases rapidly during the shearing process and remains unchanged after yielding. This study is important for the safe exploitation of hydrates under geological stratification conditions.