Pentraxin-3 (PTX3) is a multifunctional pattern-recognition molecule that is essential for immune defense, pathogen recognition, and complement activation. PTX3 is stored as a monomer in neutrophil granules, and assembles into higher-order oligomers upon immune activation, thereby enhancing its antimicrobial function. The mechanism underlying this assembly remains elusive. In this study, we employed cryo-electron microscopy to resolve multiple high-resolution structures of PTX3 in octameric and tetrameric forms, as well as medium-resolution structures in dimeric and hexameric forms. Structural analysis revealed that PTX3 oligomerization is driven by dimeric units stabilized by C-terminal interchain disulfide bonds, and the N-terminal disulfide bonds facilitate further assembly into larger oligomers. This hierarchical assembly is crucial for the activation of the classical complement pathway. These findings offer critical insights into the assembly mechanisms and structural complexity of PTX3 and pave the way for novel therapeutic developments targeting PTX3.