An automatic isolation system for head and tail filaments comprises front units and rear units. A single rear unit corresponds to at least two front units, and only one filament barrel is arranged ina single front unit. Each front unit comprises a plurality of raw filament nozzles, a plurality of filament guide wheels, a raw head device, a traction wheel and the filament barrel. The raw filamentnozzles and the filament guide wheels are in one-to-one correspondence. The filament guide wheels are located at downstream positions of the raw filament nozzles. Speed detectors are arranged on the filament guide wheels. The traction wheels are located at downstream positions of the filament guide wheels. The filament barrels are located at downstream positions of the traction wheels. Each rear unit comprises a bundle collection wheel, a first drafting wheel and a packaging device. The filament barrels of the front units are located at upstream positions of the bundle collection wheels, the first drafting wheels are located at downstream positions of the bundle collection wheels, and the packaging devices are located at downstream positions of the first drafting wheels. The automatic isolation system has the advantages of good detection effect on the head and tail filaments, less application limitation and small application range.