PKUNIFTY (PeKing University Neutron Imaging FaciliTY), a thermal neutron imaging facility based on a 2 MeV RFQ accelerator, has been constructed at Peking University. Its deuteron injector, which consists of a 2.45 GHz permanent magnet electron cyclotron resonance (PMECR) deuteron ion source and a two-solenoid low energy beam transport (LEBT), aims at producing and delivering 50 mA, 50 keV deuteron beam with a duty factor of 10% (1 ms, 100 Hz). In the preliminary tests of RFQ accelerator, the ECR ion source and LEBT are required to operate at various duty factors (from 1% to 10%). The deuteron ion source has been tested with different pulse widths for this reason. In order to optimize the transmission parameters, the beam current at the exit of RFQ as a function of solenoids tuning and steering magnets tuning are carefully studied. The beam emittance at the entrance of RFQ has been measured with space charge compensation by different argon gas (RG) pressure from 1.6 × 10(-4) Pa to 4.7 × 10(-3) Pa. The measuring results show the best compensating pressure is 3.5 × 10(-3) Pa with a minimal normalized rms emittance of 0.12 pi mm mrad. During the commissioning, we found the purity of deuteron gas is an important factor which severely affects ECR discharge and plasma intensity inside the ion source chamber. The detailed experimental results obtained during the commissioning are discussed in this paper.