The present invention relates to a pneumatic transport system of granular material, destined to convey granular material from one or more storage containers T to one or more processing machines M, comprising: - at least one loading device 10 of the granular material, provided with a collection tank 20 of the granular material; - at least one conveying duct 100 of granular material which fluidically connects the collection tank to at least one container; and - means 110, 35 of generating inside the conveying duct a flow of granular material. The system comprises for each loading device at least one sensor 51, 52 to detect vibrations induced by the material being loaded inside the loading device. Such at least one sensor is arranged in the proximity of or at the loading device and generates time signals of the vibrations that may be correlated to the mass of granular material which is progressively being loaded in the tank or to the volume of the tank being progressively filled by the granular material. The invention also relates to a control method of a pneumatic transport system of granular material.