Natural pigments have high safety and are widely used in food, cosmetics and medicine. However, at present, sources of natural pigments are extremely scarce, especially those from microorganisms. In this study, we isolated a fungus from a polar soil sample that produces purplish-red pigment and is safe and non-toxic. More importantly, the color of this pigment is very similar to the high-end pigment carminic acid, so this pigment has the potential to replace carminic acid. Besides, we obtained a strain with high yield of red pigment by ARTP (Atmospheric and Room Temperature Plasma, ARTP) mutagenesis, and explored the molecular mechanisms of high yield of red pigment. We found that the cell wall integrity (CWI) plays a critical role in the secretion of this red pigment, and identified the function of rho1 and bck1 in this fungus, which are critical genes in CWI pathway. The deletion of rho1 or bck1 significantly promote the secretion of red pigment. The Δrho1 and Δbck1 strains exhibited reduced contents of cell wall components and transcription of related genes, such as chitin and β-1,3-glucan, and the cell wall stress response was also significantly affected in these two strains. What is more noteworthy is that the overexpression of chitin synthase CHS3 hinders pigment secretion, which further confirms the role of cell wall integrity in pigment secretion. Our findings revealed the relationship of CWI pathway and pigment secretion in polar microorganism, which is of great significance for the exploitation and utilization of polar microbial resources.