The invention relates to a low-temperature vapor deposition method for a carbon-based super-lubricating thin film with an onion structure. The method comprises the following steps of (1) carrying out ultrasonic cleaning on silicon substrate by using acetone and absolute ethyl alcohol, and transferring the silicon substrate to a coating cavity; (2) vacuumizing until the vacuum degree is smaller than 4.0*10<-3> Pa; (3) cleaning under the following conditions: introducing Ar until the air pressure is 2-3 Pa, applying a negative bias voltage of -1000 to -1200 V to the silicon substrate to carry out plasma glow cleaning for 10 min; and (4) depositing the carbon-based super-lubricating thin film with the onion structure, namely keeping the bias voltage at -500 to -1000 V, the frequency at 3.5 KHz and the duty ratio at 15-25%; and keeping the air flow of Ar at 80-200sccm, the CH4 flow at 40-50sccm, the air pressure at 0.45-0.5 Pa, the target power at 800-900 W, the deposition time within 1 h and the deposited thin film thickness at about 1 mu m in the deposition process. The carbon-based super-lubricating thin film with the onion structure, prepared by using the low-temperature vapor deposition method, has the advantages of high hardness, excellent chemical inertness, low frictional coefficient, good wear resistance and the like.