Commercial sterility does not guarantee the sustained stability of ultrahigh temperature (UHT) milk over 6 months shelf life. We explore the microbiota presented in normal (SZ) and quality deteriorated UHT milk (QY and WY) products from the same brand. Based on high-throughput sequencing research results, 11 phyla and 54 genera were identified as dominant microbiota. Pseudomonas, Streptococcus, and Acinetobacter as core functional microbiota significantly influenced the UHT milk quality properties. Moreover, principal component analysis (PCA) and multivariate analyses were used to examine the quality characteristics, including 11 physicochemical parameters, 10 fatty acids, and 2 enzyme activities, in normal and quality deteriorated UHT milk. We found that the abundance of Pseudomonas increased in quality deteriorated milk (WY) and showed a significant positive correlation with heat-resistant protease content. Acinetobacter in quality deteriorated milk (QY) also considerably contributed to the content of heat-resistant lipase, which resulted in spoilage deterioration of UHT milk.