Objective To screen the active antidiarrheal components of salt-processed Alpiniae oxyphyllae Fructus-Foeniculi Fructus medicines (YZYH) and investigate its pharmacological basis and quality markers by examining its “spectrum-effect” relationship. Methods A spleen and kidney yang deficiency model of diarrhea was established in rats. The pharmacodynamic indexes of YZYH in petroleum ether, ethyl acetate, and water fractions were measured,including behavioral indicators such as body weight, anal temperature, diarrhea incubation period (DIP), diarrhea index (DI), and biochemical indicators such as nitric oxide synthase (NOS), cGMP, and creatinine phosphokinase (CPK).We analyzed the components of YZYH by high performance liquid chromatography, and analyzed the “ spectrum-effect”relationship between the chemical components and the antidiarrheal efficacy indicators using the grey correlation method. Results Compared with the blank control group, rats in the model group developed watery stools after 15 days, which was the key pathological index of the main syndrome of diarrhea. Rats in the model group also developed abdominal distension,loss of appetite, and back arching, as secondary symptoms of spleen and kidney yang deficiency diarrhea. Administration of the therapeutic drugs improved both the main and secondary symptoms of diarrhea. The positive drug and YZYH-M significantly prolonged DIP (P<0. 01) and decreased DI (P<0. 01) after 28 days. These key indexes of diarrhea, as well as body mass, 24 h food intake, water intake, anal temperature, and the serum biochemical indexes NOS, cGMP, CPK were all improved in the positive drug and YZYH-M groups. Examination of the spectral effect relationship showed that anisaldehyde, chromatographic peak 4, and other components were correlated with the pharmacodynamic indexes of DIP,DI, NOS, cGMP, and CPK. Conclusions The ethyl acetate fraction was the active antidiarrheal fraction of salt-processed Alpiniae oxyphyllae Fructus-Foeniculi Fructus medicines. It acts by inhibiting gastrointestinal hyperfunction, regulating energy metabolism and immunity. Ingredients such as anisaldehyde and peak 4 served as quality indicators for its antidiarrheal effect.