The polarimetric response of full-polarimetric ground penetrating radar (FP-GPR) from anisotropic media is a pressing issue to be investigated. It can improve the detection accuracy of the targets in the anisotropic media and can also provide effective ways to detect anisotropic targets. In this paper, we focus on the FP-GPR signals from uniaxial bi-anisotropic media, i.e. the complete case that both the permittivity and the conductivity of the background media are anisotropic. Based on the propagation characteristics of electromagnetic waves in the anisotropic media and the transmission coefficients on the surface of the media, we construct a mathematical relation between the measured scattering matrix affected by anisotropies and the real scattering matrix, derive a coefficient to characterize the polarization rotation(PR) effects, and proposed a diagonal matrix for target decomposition analyses. The computation results indicate that ε <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><i>z</i></sub> /ε <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><i>x</i></sub> , σ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><i>z</i></sub> /σ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><i>x</i></sub> , and antenna interval have complex effects on the PR coefficient and the H-Alpha decomposition results of three types of typical targets. Multiple 3D FP-GPR simulations on a series of uniaxial bi-anisotropic models verified the results.