The anisotropy in the microwave conductivity of the ortho-II YBa2Cu3O6.50 is studied within the kinetic energy driven superconducting mechanism. The ortho-II YBa2Cu3O6.50 is characterized by a periodic alternative of filled and emptyb-axis CuO chains. By considering the CuO chain induced extended anisotropy impurity scattering, the main features of the anisotropy in the microwave conductivity of the ortho-II YBa2Cu3O6.50 are reproduced based on the nodal approximation of the quasiparticle excitations and scattering processes, including the intensity and lineshape of the energy and temperature dependence of theâ-axis andb-axis microwave conductivities. Our results also confirm that theb-axis CuO chain induced impurity is the main source of the anisotropy.