Abstract: In order to reflect the correlation between the biochemical parameters and traits of Neoporphyra haitanensis conchocelis and establish a biochemical evaluation system for the selection of new varieties, the photosynthetic pigments and growth indicators of the conchocelis of 5 varieties/strains were compared, and the contents of floridosides, mycosporine-like amino-acids (MAAs) and phytohormones were determined by liquid chromatography-mass spectrometry. The results showed that phycobiliprotein and chlorophyll a were positively correlated with the net photosynthetic oxygen release rate and the relative growth rate, and were related to the high-yield characteristics of N. haitanensis. The conchocelis of Zhedong 2 (ZD2), Shenfu 2 (SF2) and Minfeng 1 (MF1) had higher phycoerythrin content and relatively fast growth rate. Floridosides were related to the high-temperature resistance of N. haitanensis. MF1 and MF2 were dominated by isofloridosides, while other varieties/strains were dominated by floridosides. MAAs is related to resistance to ultraviolet radiation. MF1 and MF2 contained high Shinorine content, and the content of MAAs in MF2 was much higher than that of the other 4 varieties/strains, reflecting the high temperature tolerance and UV resistance of the characteristics of southern varieties of Minfeng. Four plant hormones were found in the conchocelis of N. haitanensis, including isoprene adenine, isoprene adenosine, trans-Zeatin nucleoside and brassinolide, but the relationship between the hormones and production traits was not clear. In summary, the parameters of phycobiliprotein, chlorophyll a, floridosides and MAAs are closely related to the different biological characteristics of N. haitanensis. This study constructed a set of feasible evaluation index system for the selection and cultivation of the conchocelis of new varieties of N. haitanensis.