The screening of high-producing strains is a bottleneck in bioengineering. Although some of the high yield strains can be selected by comparing the color of cell colonies with eyes, the eyeballing method was rough and irrational. A practical strain selection method has been developed by sensing cellular metabolite in cell colonies with RGB color test system, which allows a better characterization of stains. The color of Phaffla rhodozyma cell colonies was measured by RGB color test system and RGB value of cell colonies' colors was employed to estimate the content of astaxanthin in cells. With this platform, the high-producing strains were selected by comparing the RGB value of cell colonies. The method of sensing cellular metabolite in cell colonies with RGB color test system provides a new approach for high-throughput screening of desired strain.