Crab burrows have a unique structure, which is essential for ecosystem functions and for the survival and reproduction of crabs in tidal salt marshes. Studies on the distribution characteristics of the burrows, and corresponding factors that influence such features, provide an important basis to reveal the ecosystem functions of crabs and their burrows. In October 2015, we conducted surveys on crab burrows in three typical salt marsh habitats in the northern tidal flat of Chongming Island in the Yangtze estuary, including the Phragmites australis habitat, Spartina alterniflora habitat, and P. australis-S. alterniflora mixed habitat. In each habitat, the characteristics of crab burrows and related factors, including macrobenthos, vegetation, and sediment, were surveyed. The results indicated that the type of the habitat influenced the crab burrow distributions and their related factors. Burrow densities and opening diameters were significantly different among the different habitats (P < 0.05). The burrow density in P. australis habitat was significantly higher than that in S. alterniflora habitat (P < 0.05), whereas the burrow opening diameter in S. alterniflora habitat was significantly greater than that in P. australis habitat (P < 0.05). There was no significant difference in biomass and density of macrobenthos, and belowground biomass of plants among the different habitats (P > 0.05). However, there were significant differences in shoot density, height, aboveground biomass of the vegetation, as well as water content, pH, and oxidation-reduction potential of the sediment among the different habitats (P < 0.05). The differences among the habitats in the total carbon content, total nitrogen content, and median particle diameter of the sediments varied with depth. The different combinations of habitat factors resulted in a variation in the distribution characteristics of crab burrows. In the present study, although the combination of several selected factors was significantly correlated with the crab burrow distribution characteristics, the coefficient was relatively low. Therefore, there could be other factors that were not included in the surveys that also affected burrow distribution characteristics. Further study should extend the scope of the factors and strengthen the comprehensive analysis.