Thermostable enzymes in raw milk can seriously affect the quality stability of the shelf life of products. However， the main sources and contamination pathways of thermostable enzymes have been debated. In this study， metagenomic technology was performed to analyze the microbial community composition and gene abundance of extracellular protease (EC 3.4.24.40) and lipase (EC 3.1.1.3) in environmental samples (barn bedding soil， TMR feed) and fresh milk samples (the first three milk， after the first three of milk， and raw milk of storage tank) from a farm in China. This study aimed to investigate the source of thermostable enzyme contamination of raw milk in milk storage tanks. The results of diversity analysis showed that the abundance of typical psychrophilic bacteria such as Pseudomonas(1.57%) and Acinetobacter(1.56%) in the barn bedding soil was much higher than that of the other samples. It was much higher than the first three milk (0.26%， 0.54%). Through gene analysis of microbial enzyme production， the microorganisms that thermostable enzymes in raw milk of storage tank were mainly from psychrophilic bacteria， Pseudomonas and Acinetobacter. The abundance of extracellular protease-producing genes in each sample was barn bedding soil: 8.71 and the first three milk: 0.18； the abundance of extracellular lipase-producing genes in each was barn bedding soil: 16.19， TMR feed: 0.33， the first three milk: 0.18， after the first three of milk: 0.39 and raw milk of storage tank: 0.22. In addition， the lipase gene of raw milk in storage tanks had the lowest gene duplication of 57.14% during the raw milk collection line. In addition， microorganisms and their psychrophilic bacteria contaminate the teats of cows through barn bedding soil. Then， they enter the raw milk collection line and cause contamination during milking. This study provided a theoretical and data basis for the effective prevention and control of thermostable enzymes contamination in raw milk.