Marine microplastic pollution gradually becomes a global environmental problem. Nanoplastics are much smaller than microplastic and can migrate in the marine environment, bringing higher environmental risks. In this study, carboxyl-modified PS nanoplastics were selected to explore the transport mechanism of nanoplastics in marine sediments. Results showed that the recovery rate of PS nanoplastics in marine sediments (C/C 0 = 0.43) was significantly lower than that in quartz sand (C/C 0 = 0.70). Three reasons are given as follows: (1) the porosity (0.28) of the sediment was lower than that of saturated quartz sand (0.38), resulting in a stronger blocking effect in sediment; (2) the heteroaggregation of PS nanoplastics and marine sediments inhibited their transport; (3) the components of marine sediments (e.g., minerals) promoted the interaction between nanoplastics and sediments. This study gave insights into the transport behavior and mechanism of PS nanoplastics in sediments, which would help to further understand the transport and fate of nanoplastics in the marine environment.