Tetramethylpyrazine (TTMP) is an important aroma compound in the sesame-flavored Chinese liquor, baijiu. Similar to other traditional spontaneously fermented foods, it is difficult to directionally increase the key aroma compound in situ fermentation system of baijiu without changing its sensory profile. The assembly of the starting microbial community for fermentation by using a functional starter provides a promising solution which needs careful manipulations. This study aimed to increase TTMP concentration in baijiu using the functional starter inoculated with the indigenous strain B. amyloliquefaciens XJB-104 with high TTMP production ability. After inoculation, the relative abundance of Bacillus in the initial stage of fermentation increased from 82.14% to 88.47%. The TTMP concentration increased by about 26 and 24-fold in the fermented grains (zaopei) and baijiu respectively compared with controls. Moreover, the quality of baijiu was improved according to sensory analyses. In addition, correlation analysis confirmed that the increased TTMP content in baijiu was due to the successful assembly of the initial fermentation microbiota after the inoculation of B. amyloliquefaciens.