The invention discloses an operation method based on a roadbed filling intelligent command system and system thereof. The method comprises the following processes of construction preparation, construction planning, filling operation, paving and leveling operation, unmanned rolling operation of a road roller, slope finishing operation and quality acceptance. According to the method, with an intelligent roadbed filling command system as a core, theoretics and technologies of BIM, big data, Beidou positioning, automatic control, informatization detection, Internet of Things and the like are comprehensively applied to achieve dynamic management, automatic paving guidance, automatic fine leveling control, unmanned rolling compaction and automatic slope finishing guidance of filler transportation under unified scheduling of a command system, so that continuous detection of roadbed compaction quality, filler grading and automatic detection of moisture content are realized, and a novel digitaland intelligent high-speed railway roadbed filling technology is formed; the roadbed filling quality is effectively guaranteed, the operation efficiency is improved, and the traditional operation mode of roadbed construction is changed.