The Xialu chert, which contains abundant biological information, were investigated by major element analysis, micro-Raman, SEM and EPMA. The results show that SiO2 content of chert is 84.12%-93.08%, averaging 89.84%. The close packed structures of low degree crystallinity of quartz indicate the hydrothermal origin. SiO2 of modern hot springs exhibit loose silica pellets and nodular, beaded structures. Under polarization microscope, the presence of biological skeleton structures indicate that biological activities are involved in the hydrothermal deposition, which correspond to the geochemical characteristics: w(SiO2)/ w(K2O+Na2O), w(SiO2)/w(Al2O3) and w(SiO2)/w(MgO), with average values of 295.29, 68.88 and 284.45, respectively. SiO2 is enriched in the organism(radiolarian) centers, the degree order of SiO2 within the biologic structures is much higher than that of outside. The impurity minerals albites are formed earlier than the original deposition. Kaolinites, feldspars and mixture of organic materials display lower degree of crystallinities and accumulate as vermicular aggregates.