The methanol-to-olefins (MTO) process is becoming the most important non-petrochemical route for the production of light olefins from coal or natural gas. Maximizing the generation of the target products, ethene and propene, and minimizing the production of byproducts and coke, are major considerations in the efficient utilization of the carbon resource of methanol. In the present work, the heterogeneous catalytic conversion of methanol was evaluated by performing simultaneous measurements of the volatile products generated in the gas phase and the confined coke deposition in the catalyst phase. Real-time and complete reaction profiles were plotted to allow the comparison of carbon atom economy of methanol conversion over the catalyst SAPO-34 at varied reaction temperatures. The difference in carbon atom economy was closely related with the coke formation in the SAPO-34 catalyst. The confined coke compounds were determined. A new type of confined organics was found, and these accounted for the quick deactivation and low carbon atom economy under low-reaction-temperature conditions. Based on the carbon atom economy evaluation and coke species determination, optimized operating conditions for the MTO process are suggested; these conditions guarantee high conversion efficiency of methanol.