Accelerator Based Neutron Sources (ABNS) have been studied for their utility in materials research as well as for boron neutron captured therapy. By making significant efforts to study the (p,n) and (d,n) nuclear reactions, the specifications of the accelerator system have been determined. In this paper, we compare the design results for two types of radio frequency quadrupole (RFQ) accelerators to provide proton and deuteron beams, respectively. Both systems consist of an electron cyclotron resonance (ECR) ion source, a low-energy beam transport system, an RFQ accelerator, a medium-energy beam transport system, a Be target, and a moderator system. In order to achieve a compact accelerator system at a reasonable cost, different requirements must be applied to the design of RFQ accelerators. The proton RFQ has been designed with an operation frequency of 352 MHz, up to 4 MeV acceleration, 10 mA beam intensity, and a continuous-wave (CW) operation mode to achieve 0.84 × 109 n/(s/cm2) of neutron production. However, the deuteron RFQ has been designed with an operation frequency of 200 MHz, up to 2.5 MeV acceleration, 15 mA of beam intensity, and a CW operation mode to achieve 1.02 × 109 n/(s/cm2) of neutron production. In this paper, we describe the merit of the deuteron based neutron source by comparing two types of the RFQ accelerators for proton and deuteron beams including the common system of the ECR ion source and Be target in detail.