The mud shrimp Austinogebia edulis, being abundant in the intertidal zone of western Taiwan, constructs deep burrows (>1 m). This study highlights the potential of mud shrimps to modify sediment characteristics of the tidal flat by its burrowing behavior. We studied the structure of the burrow wall, compared the difference in the sediment composition of the burrow and the background sediment, and compared the organic content inside the burrow wall. This study was carried out from September 2015 to November 2016 in three areas of the western coast of Taiwan, namely Shengang, Hanbow, and Wangong. The present study found significant differences between burrow wall and the burrow lumen. The diameter of the burrow wall was double as wide as the inner burrow lumen at the opening and gradually increased to 10 times of the burrow lumen at 30 cm depth. The burrow wall of A. edulis showed low permeability and increased the sheer strength. Statistically, a significant difference was noticed in the comparison between the sediment composition of the burrow wall and the background (p < 0.05, Student's t-test). An accumulation of 3.63 for fine sand (t = -5.22, p < 0.001, fine sand) and 9 for clay (t = -25.01, p < 0.001, clay) was found in the upper burrow wall of A. edulis. This indicated that they somehow chose finer particles to build burrows. This will gradually change the sediment distribution-vertically and horizontally. The burrow wall consisted of a 24 times higher organic matter content than one individual of mud shrimp. The burrow may provide organic material as a potential food source. The mud shrimp thus transforms the sediment characteristics as an ecological engineer, which is expected to have a significant ecological impact on the ecosystem.