Olanzapine is a marketed antipsychotic agent for treatment of both positive and negative symptoms of schizophrenia. The chemical synthesis of olanzapine drug substance involved the reaction of thienobenzodiazepine hydrochloride with N-methylpiperazine. During the manufacture of olanzapine, two unknown impurities were present in pilot batches in the range of 0.08–0.22% based upon HPLC analysis. These unknown impurities were enriched from the mother liquor of reaction by preparative HPLC, and characterized by UV, FT-IR, LC–MS/TOF, 1D-NMR (1H, 13C, DEPT), 2D-NMR (1H-1H COSY, HSQC, HMBC, ROESY) and single-crystal X-ray diffraction analysis. Based on the complete spectral analysis and knowledge of the synthetic route of olanzapine, these two new impurities were identified as 2-methyl-4-(4-methyl piperazin-1-yl)-10-((methylthio)methyl)-thieno[2,3-b][1,5] benzodiazepine (impurity-I) and 10-(3-(1H-benzo[d]imidazol-2-yl)-5-methylthiophen-2-yl)-2-methyl-4-(4-methyl piperazin-1-yl)-thieno[2,3-b][1,5]benzodiazepine (impurity-II). Finally, prospects to the formation and controlling of impurity-I and II were discussed in detail.