Objective To screen the antidiarrheal active components of salt-processed Alpiniae oxyphyllae Fructus -Foeniculi Fructus medicines (YZYH), and speculate on its pharmacological substance basis and quality markers through the study of the “spectrum-effect” relationship. Methods A model of diarrhea due to spleen and kidney yang deficiency was established in rats, and the pharmacodynamic indexes of YZYH on petroleum ether, ethyl acetate, and water fractions were measured, including behavioral indicators such as body weight, anal temperature, diarrhea incubation period, diarrhea index, and biochemical indicators such as NOS, cGMP, and CPK; Establish HPLC chromatograms of different parts of YZYH, and use grey correlation method to analyze the “spectrum-effect” relationship between the chemical components of each part of YZYH and the antidiarrheal efficacy indicators. Results In the aspect of pharmacodynamics, the ethyl acetate fraction had a better regulatory effect on the activities of DIP, DI, and serum NOS, cGMP, CPK in model rats compared to other treatment groups; In terms of the study of the “spectrum-effect” relationship, the correlation between components such as anisaldehyde and chromatographic peak 4 with the five efficacy indicators of DIP, DI, NOS, cGMP, and CPK was strong. Conclusion The ethyl acetate fraction was the active anti diarrhea fraction of salt-processed Alpiniae oxyphyllae Fructus -Foeniculi Fructus medicines. Its mechanism may be realized by regulating gastrointestinal peptide hormones such as MTL and GAS, inhibiting gastrointestinal hyperfunction, regulating energy metabolism and immunity, and cytoprotection; The ingredients such as anisaldehyde and peak 4 served as the material basis for its antidiarrheal effect, and anisaldehyde and peak 4 could be used as quality indicators for the medicines.