A medication dispensing system, method and non-stationary computer readable recording medium thereof are provided. The medication dispensing system includes a medication dispenser adapted to accommodate a plurality of medicine units for dispensation. The medication dispenser includes a user interface unit, an identifier, and a processor. The identifier is adapted to communicate with an identifiable unit. The processor is coupled to the user interface unit and the identifier. The processor is configured for obtaining an identification data recorded in the identifiable unit through the identifier and identifying a user identity related to the medicine units based on the identification data, receiving a first command through the user interface unit, wherein the first command includes a daily routine schedule, scheduling a medication schedule according to the daily routine schedule after the user identity is identified, and executing a medicine outputting operation and a reminding operation according to the medication schedule.