The invention relates to a high-vacuum automatic sample injection system for trace gas. The system comprises an automatic control device, a main vacuum pipeline, a sample storage pot I, a sample storage pot II and a metal leaking hole, wherein a sample injection opening is formed in the main vacuum pipeline; the front end of the main vacuum pipeline extends into a gas device, and the tail end of the main vacuum pipeline is connected with a high-vacuum mass spectrometer, the sample storage pot I and the sample storage pot II; a vacuum branch pipe I and a vacuum branch pipe II are arranged on the main vacuum pipeline; the vacuum branch pipe II is connected with a molecular pump; the molecular pump is connected with a mechanical pump; four pneumatic high-vacuum valves are arranged on the main vacuum pipeline; another two pneumatic high-vacuum valves are arranged on the vacuum branch pipe I and the vacuum branch pipe II; another two pneumatic high-vacuum valves are arranged between the sample storage pots I and II and the main vacuum pipeline; the sample storage pots I and II are connected with the main vacuum pipeline; the automatic control device comprises a computer, an air compressor, a relay board and a power supply; the relay board is connected with eight electromagnetic valves connected with the eight pneumatic high-vacuum valves in a one-to-one correspondence manner respectively. The invention also discloses a use method for the system. The system is easy to measure and control and convenient to use.