Pseudostellaria heterophylla is an important traditional Chinese herbal medicine with vast clinical consumption because of its positive effects. To date, changes in the metabolite composition of P. heterophylla have been well documented; however, the molecular differences between cultivated P. heterophylla and its wild-type are still unknown. The aim of this study was to investigate differences in cultivated and wild P. heterophylla. Due to the lack of a genomic database, we used high-throughput transcriptomic and proteomic technologies to identify proteins in the herb. Isobaric tags for relative and absolute quantification (iTRAQ) MS/MS were used to detect statistically significant changes between cultivated and wild P. heterophylla. We detected 3775 proteins; 332 showed differential accumulations across two different ecotypes of P. heterophylla. 71 significant differential expressions of proteins were selected based on GO annotations, KEGG, STRING analysis, and expression level. Quantitative real-time PCR analysis confirmed the authenticity and accuracy of the proteomic analysis. The results indicated that the carbohydrate and cellular amino acid metabolisms in cultivated P. heterophylla were weaker than those in its wild-type; seven important proteins were found to regulate sucrose and amino acids. This will provide the basic information for exploring the cause of differences in secondary metabolites in different ecotypes of P. heterophylla and the protein mechanism of its quality formation.This study combined a transcriptome, proteome, and metabolism approach for analyzing differentially expressed proteins of cultivated and wild P. heterophylla and established the relationship between significantly differentially expressed proteins and differential chemical components in non-model plants. The results of proteomic analysis provide the basic information for exploring the quality forming process, which will demonstrate, and provide guidance for, the study of effective constituents of P. heterophylla and its quality formation mechanism.