Boron neutron capture therapy (BNCT) is a cancer treatment modality using a nuclear reactor and a boron compound drug. In Taiwan, Tsing Hua open-pool reactor (THOR) has been modulated for the basic research of BNCT for years. A new BNCT beam port was built in 2004 and used to prepare the first clinical trial in the near future. This work reports the microdosimetry study of the THOR BNCT beam by means of the tissue equivalent proportional counter (TEPC). Two self-fabricated TEPCs (the boron-doped versus the boron-free counter wall) were introduced. These dual TEPCs were applied to measure the lineal energy distributions in air and water phantom irradiated by the THOR BNCT mixed radiation field. Dose contributions from component radiations of different linear energy transfers (LETs) were analyzed. Applying a lineal energy dependent biological weighting function, r(y), to the total and individual lineal energy distributions, the effective relative biological effectiveness (RBE), neutron RBE, photon RBE, and boron capture RBE (BNC RBE) were all determined at various depths of the water phantom. Minimum and maximum values of the effective RBE were 1.68 and 2.93, respectively. The maximum effective RBE occurred at 2cm depth in the phantom. The average neutron RBE, photon RBE, and BNC RBE values were 3.160+/-0.020, 1.018+/-0.001, and 1.570+/-0.270, respectively, for the THOR BNCT beam.