The Sanshui Basin (SSB) is located at the northern continental margin of the South China Sea and characterized by a continental rift basin. The bimodal volcanic rocks in SSB record the early Cenozoic magmatic activity in the South China Block, on the magmatic evolution process of bimodal volcanic rocks are poorly understood. Clinopyroxenes in bimodal volcanic rocks in the SSB provide an opportunity to investigate the magma process during magma ascent. We classified nine types of clinopyroxene phenocrysts according to the different compositions and textures types in cogenetic basalt-trachyandesite-comenditic trachyte, the composition of unzoned clinopyroxene have an evolution sequence of diopside- hedenbergite- aegirine with the decrease of Mg#, and the trace element contents of unzoned clinopyroxenes also increase systematically during magma evolution, indicating that the genesis of clinopyroxene dominated by fractional crystallization in a closed magma system; however, the clinopyroxenes with reverse zoning and multiple zoning record the process of magma mixing and recharge indicating an open magma system. Whilst fractional crystallization is the dominated process, magma mixing, recharge, and crystal settling complicate magma evolution. Thermobarometric calculations show that clinopyroxene phenocrysts in bimodal volcanic rocks of SSB are distributed in the whole crust during magma ascent. We have established a magma plumbing system, which provides a new constrain for the complex magmatic evolution history in the SSB by detailed mineral-scale analysis.