The beam commissioning of Separated Function RFQ (SFRFQ) accelerator, which can gain high accelerating efficiency and enough focusing strength for low energy high current beam, is presented. In order to demonstrate the feasibilities of this novel accelerator, a prototype cavity was designed and constructed. The O beam was accelerated from 1MeV to 1.6MeV by SFRFQ cavity. A triplet was constructed for the transverse beam matching between the 1MeV ISR-RFQ 1000 and SFRFQ. A capacitance frequency tuning system and RF phase shifter were used to keep SFRFQ cavity working at the same frequency of ISR RFQ at the right phase. The whole RFQ accelerator system and the preliminary beam test results are presented in this paper.