As an important halophyte in the Yellow River Delta, the Amaranthaceae C3 Suaeda salsa (L.) Pall. has attracted much attention for the “red carpet” landscape, and could be simply divided into red and green phenotypes according to the betacyanin content in the fleshy leaves. However, S. salsa has not been sequenced yet, which limited people’s understanding at the molecular level. We constructed a high-quality chromosome-level reference genome by combining high-throughput sequencing, PacBio Single Molecule Real-Time (SMRT) sequencing, and Hi-C sequencing techniques with a genome size of 445 MB and contigs N50 of 2.94 Mb. Through the annotation of the reference genome, a total of 288.23 Mb of the repeating elements (64.76% of the total genome size) and 23,965 protein-coding genes were identified. Comparative genomics indicated that S. salsa undergone a WGD event about 146.15 million years ago (mya), and the estimated divergence time between S. salsa and S. aralocaspica was about 16.9 mya. A total of four betacyanins including betanidin, celosianin II, amaranthin and 6’-O-malonyl-celosianin II were identified and purified in both phenotypes, while two significantly up-regulated betacyanins (celosianin II and amaranthin) may be the main reason for the red color in red phenotype. In addition, we also performed transcriptomics and metabolomics in both phenotypes to explore the molecular mechanisms of pigment synthesis, and a series of structural genes and transcription factors concerned with betacyanin production were selected in S. salsa.