Variations in vegetation composition and structure are significant signals of the succession of mudflat ecosystems and have important indicative roles in mudflat ecosystem degradation. Due to poor accessibility of vast even mudflat areas, variation in vegetation composition and structure across mudflat areas remains unclear in the Yellow River Delta (YRD), China. We provided an UAV multispectral orthomosaic with 10 cm ground sample distance to classify and compare the vegetation composition and structure across mudflat areas in the YRD. The vegetation classification overall accuracy achieved 95.0%. We found that although a significant difference (p < 0.05) was checked out in terms of the Shannon–Wiener diversity index (from 1.33 to 0.92) and evenness index (from 0.96 to 0.66) among the eight subareas from land to sea, all four dominant vegetation communities (S. salsa, L. bicolor, T. chinensis, and P. australis) were discovered at all eight subareas. Our findings support the idea that the regional environment and local microtopography are the predominant forces for variation in vegetation composition and structure across mudflat areas. From the perspective of vegetation restoration and conservation, changing the local microtopography will be an interesting way to enhance the vegetation diversity of the mudflat ecosystems in the YRD.