Phycocyanin is a biliprotein that has been used as a natural food colorant due to its brilliant color. However, their application is limited by their poor stability. In this study, biosynthesis pathways of two phycocyanin holo-β subunits, CpcBA from mesophilic Arthrospira platensis and CpcBT from thermophilic Thermosynechococcus elongatus BP-1, were constructed in Escherichia coli. Coexpression of ferredoxin (Fd), Fd-NADP+ reductase (FNR), and NADP-specific glutamate dehydrogenase (gdhA) enabled full chromophorylation of these recombinant CpcBs in recombinant E. coli. These fully chromophorylated CpcBs were visually redder and had higher hydroxyl radical and peroxyl radical scavenging activities than the partially chromophorylated CpcBs. Comparative study on thermostability showed that at high temperature the CpcBT had lower denature rate constants and longer half-life values than the CpcBA. Both proteins were stable at acidic pH (3.0–6.6), except for the CpcBA at pH 3.0. Under a combinational treatment of acid pH and heat, CpcBA showed remarkable losses (93.6–98.4%) while CpcBT showed much less losses (20.0–49.6%). All the results indicated that CpcBT was a stable phycocyanin and could potentially be developed as an excellent colorant in the food industry.