A diffuser structure and a manufacturing method thereof are disclosed. The diffuser structure includes a substrate, a plurality of throughholes, and a glue layer. The throughholes are perpendicularly formed in the substrate. Each throughhole includes a gas-in part, a gas-out part, and a connecting part for connecting the gas-in part to the gas-out part. The glue layer is formed on a side wall of each gas-out part, and a thickness of the glue layer is between 1 μm and 11 μm. The present invention can solve a problem that particles are periodically generated after a periodic self-cleaning function is implemented in a plasma-enhanced chemical vapor deposition system.