This study presents detailed microscopic observations of the Tongguanshan pluton along the Yangtze River region in south Anhui Province, obtained element concentrations of different minerals by electron probe line micro-analysis and LA-ICP-MS. Microscopic features shows there are lots of unbalanced structures in the Tongguanshan pluton, such as embedded crystal structure of plagioclases, hornblendes and acicular apatites, which reveals that the Tongguanshan pluton had undergone through one or several times of magma mixing during its formation process. EPMA results show that the plagioclase zoning is a shock zone, the large-scale zone may be due to a large-scale magmatic activity. Compositions of amphiboles indicate amphibole crystals were most probably originated from mantle or crust-mantle mixing sources. REE and trace elements results illustrate that amphiboles were also from mantle or crust-mantle mixing sources and plagioclase may form from the mixing of magma of different magmatic differentiation. Our results of element concentrations of main rock-forming minerals from the Tongguanshan pluton as well as micro-structural features do reveal the fact of mixture of crust-mantle metasomatism and crystallization kinetics process, well corresponding to former conjecture obtained through geochemical methods.