Due to human activity and global climate change, the Yellow River Delta, the youngest delta wetland in China, is suffering serious degradation. The study of hydrological connection provides new perspectives and technical support for the protection and restoration of delta wetlands. To quantify the interaction between the hydrological connection and the root–soil complex, the current study took dye-tracing experiments to examine the small-scale hydrological connectivity in soil where Phramites australis grew. The dye coverage was selected as the indicator of hydrological connectivity after preliminary analysis in this study. The main results were that (1) the strength of hydrological connectivity was negatively related to the microaggregates content, but had little to do with other soil physical properties; (2) there was a notable positive correlation between the indexes of thick root (D > 5 mm) and the dye coverage hydrological connectivity, while root biomass had little effect on hydrological connectivity; and (3) the influence of the microaggregate content dominated in the combined effect of the total surface area of the root (D > 5 mm) and the microaggregate content on hydrological connectivity in each soil layer.