A control method and pneumatic transport system of granular material, conveys granular material from storage containers to processing machines includes at least one loading device of the granular material with a collection tank of the granular material; at least one granular material conveying duct fluidly connecting the collection tank to at least one container; and a granular material flow generator inside the conveying duct. For each loading device at least one sensor detects vibrations induced by the material being loaded inside the loading device. The sensor is arranged at or near the loading device and generates time signals of the vibrations that may be correlated to the granular material mass being progressively loaded in the tank or to the volume of the tank being progressively filled by the granular material.