In this study, the nanostructured MnAPSO-34 catalysts were synthesized via different heating methods including microwave (MW) and hydrothermal (HT). The MnAPSO-34 (HT) catalyst was studied for its properties and catalytic performance in the MTO reaction and compared with unmodified SAPO-34 (HT). Furthermore, the effects of seed-assisted and microwave power were investigated in the synthesis of MnAPSO-34 (MW), and the results were compared with those prepared under conventional heating. The samples were characterized by XRD, FESEM, EDX, BET and FTIR techniques. For MnAPSO-34 prepared by hydrothermal method, Mn incorporation modified the Si distribution into the crystalline structure. The catalytic performance of SAPO-34 (HT) and MnAPSO-34 (HT) showed that the stability and light olefins selectivity are improved with Mn incorporation. The microwave power is a crucial factor for synthesis of catalysts to obtain the proper morphology and crystalline structure. Using low microwave power caused to production of irregular particles and amorphous phase. MnAPSO-34 (MW) catalyst prepared by seed -assisted microwave synthesis indicated low active sites and poor catalytic performance. As a result, the sufficient synthesis time, proper morphology and crystalline structure for hydrothermal synthesis led to special physicochemical properties and good catalytic performance.