Intertidal creek ecosystems in saltmarsh wetlands provide crucial ecological services, with burrows facilitating material exchange between these environments. Investigating burrow distribution in tidal creeks is essential, yet the underlying mechanisms remain poorly understood. Our study conducted field observations during two seasons, dividing the typical creek section into microhabitats: flat (F), gentle edge (GE), gentle slope (GS), steep slope (SS), and steep edge (SE). Comprehensive analysis of sediment samples encompassed assessments of water content, organic matter, particle size, and salinity. Burrow parameters were extracted using a deep learning method applied to sample images. Benthic biodiversity and community compositions were characterized through eDNA analysis. Our findings revealed significant variations in burrow distribution, sediment properties, and community compositions, both between and within creek sections. Temporal heterogeneity emerged as a substantial influencer of burrow characteristics, while the propensity of benthic communities to respond to topography and sediment properties constituted a chief determinant of burrow distribution. Utilizing a structural equation model based on field data, we illuminated four response pathways governing burrow distribution. Abiotic factors, especially under temporal heterogeneity, had a paramount impact, highlighting the need to explore relative biotic and abiotic influences, considering seasonal regulation. These findings establish a foundational understanding of burrow distribution and its driving mechanisms in creek ecosystems. They offer valuable insights for future field observations and research directions in this field.