In this paper, a time projection chamber (TPC) system for α radiation detection with ultra-low background is presented, which is based on Micromegas, a type of micro-pattern gaseous detector. Based on multi-dimensional information acquired by the TPC, such as the features of particle energy deposition and 3D track, the system can achieve the purpose of α identification with ultra-low background. A prototype TPC with the volume of 15 × 15 × 6.5 cm3 was developed. It was filled with a gas mixture of 95% neon and 5% isobutene at about 1 bar, and no additional shielding or control of alpha-emitting materials was employed. A low-noise high-integration electronic system based on multi-channel waveform sampling techniques was adopted to read out the anode strip signals. A test with a 241Am α source (5.5 MeV), a 49-h background test, and several other tests with weak radioactive samples in the laboratory environment were conducted. A feature selection method was designed to maximize the suppression of background events while retaining the events of interest. Test results showed that within an assumed 5 × 5 cm2 effective area in the center region of the TPC window, the background count rate of this system was lower than 1.6 × 10-3 counts per minute at 95% confidence level, while retaining the acceptance rate of about 96% for 241Am α particles.