Silicoaluminophsophate (SAPO)-34 is considered as a promising catalyst for methanol-to-olefin (MTO) reaction, because its cylinder-like cages with small 8-ring pore openings restrict the diffusion of large hydrocarbons and exceptionally give high selectivity for light olefins. However, its main drawback is rapid catalytic deactivation by heavy hydrocarbons confined inside the cages. Here, we report a facile synthetic strategy for submicro-sized cobalt (Co)-isomorphous substituted SAPO-34 with controlled Co content through milling and Co-incorporated recrystallization. Co-isomorphous substitution on the CHA framework of SAPO-34 was thoroughly proven by XRD patterns, HADDF scanning TEM images, EDS mapping images, H2-TPR profiles, and diffuse reflectance UV-Vis spectra. Regarding the modified particle size, pore structure and acidity of the as-synthesized Co-isomorphous substituted SAPO-34, evaluation of MTO reaction revealed the correlation between the catalytic lifetime and the content of Co-isomorphous substitution. As an efficient platform to overcome the intrinsically low catalytic lifetime toward MTO reaction, this work provides a versatile strategy to generate various transition metal-isomorphous substituted SAPO-34 materials on the submicro scale.