The maturation of Pixian Douban (PXDB) plays a crucial role in developing its distinctive flavor profile; however, the detailed dynamics of lipid changes and their contributions have been insufficiently explored. To address this, we conducted a comprehensive study using lipidomics, lipid building block analysis, and third-generation high-throughput sequencing techniques. Our analysis revealed significant fluctuations in 86 lipid species over a 1- to 2-year maturation period, with notable decreases in diacylglycerols and lysophosphatidylcholines containing C18:2 fatty acid chains. These lipid changes were closely linked to key microbial genera—Sphingomonas, Microbacterium, and Arthrobacter—and specific lipid subclasses. Our findings offer valuable insights into the biochemical processes driving PXDB maturation and highlight potential opportunities for targeted enhancement of its flavor quality.