In the Southwestern Tianshan, the geologic ages of many strata and their depositional environments are still poorly constrained because of complex structures. The Mada’er area is located in the Kuokesaleling belt, Southwestern Tianshan. The cherts from the former Wupata’erkan Group contain abundant radiolarian fossils, including 10 species which are identified as late Devonian to early Carboniferous in age. Eleven chert samples have SiO2 contents ranging from 88.80 wt% to 93.28 wt%, and 2.02 wt% to 3.72 wt% for Al2O3. The SiO2/Al2O3 ratios of all samples vary from 23.84 to 46.11, much lower than those of the pure cherts (80–1400). These values suggest that the cherts contain high ratios of terrigenous materials. The Al2O3/(Al2O3+Fe2O3) ratios vary between 0.64 and 0.77, whereas V and Cu concentrations range from 10.92 ppm to 26.7 ppm and from 2.15 ppm to 34.1 ppm respectively. The Ti/V ratios vary from 25.53 to 44.93. The total REE concentrations of the cherts are between 30.78 ppm and 59.26 ppm, averaging 45.46 ppm. The (La/Ce)N ratios range from 0.81 to 1.12, and 0.88–1.33 for (La/Yb)N, averaging 1.09, which suggests a continental margin environment. Consequently, it is inferred that the cherts formed in a residual sea environment during the late Devonian to early Carboniferous time, which suggests that the collision between the Karakum-Tarim and Kazakhstan-Junggar plates did not occur at the time. In addition, the regional geological information indicates that the study area experienced a post-collision stage during the early Permian, and thus it is likely that the collision between the two plates took place in the late Carboniferous.