In this paper, we investigate the effects and problems of MLLR speaker adaptation when applied to pronunciation evaluation. Automatic scoring and error detection experiments are conducted on two publicly available databases of Japanese learnersÂ’ English pronunciation. As we expected, over-adaptation causes misjudge of pronunciation accuracy. Following these experiments, two novel methods, Forced-aligned GOP scoring and Regularized-MLLR adaptation, are proposed to solve the adverse effects of MLLR adaption. Experimental results show that the proposed methods can better utilize MLLR adaptation and avoid over-adaptation.