Hierarchical SAPO-34 was synthesized hydrothermally using carbon nanotube as hard template and modified with Co and Ni by isomorphous substitution and impregnation methods. The prepared catalysts were characterized by XRD, SEM, TEM, XRF, UV–vis, NH3-TPD, H2-TPR, FTIR and N2 physisorption measurements and their catalytic performance was evaluated for transformation of methanol to light olefins (MTO). There were meaningful differences in terms of crystallinity, acidity, porosity and reducibility among the synthesized catalysts modified by impregnation and isomorphous substitution methods. In addition, the ethylene and propylene yields and the catalytic longevity were strongly dependent on Ni and Co avidities as well as on the modification procedure. The results indicated that compared to the unmodified hierarchical SAPO-34, the catalyst modified with Ni by means of isomorphous substitution improved the yield of ethylene while methane production was promoted over SAPO-34 impregnated with Ni. On the other hand, the Co-containing SAPO-34 samples enhanced the production of both ethylene and propylene relative to the unmodified mesostructured SAPO-34 and these modifications prolonged the catalyst lifetime. These changes in the catalytic behaviors could be ascribed to the changes in the acid sites and porous structure.