This study focused on developing an effective cell wall-breaking method for Phaffia rhodozyma, followed by utilizing subcritical fluid extraction to isolate, extract, and concentrate astaxanthin from the complex fermentation products of P. rhodozyma. A comprehensive comparison of seven distinct methods for disrupting cell walls, including dimethyl sulfoxide treatment, lactic acid treatment, sodium hydroxide treatment, β-glucanase enzymatic digestion, β-mannanase enzymatic digestion, and a combined enzymatic treatment involving both β-mannanase and β-glucanase was conducted. The results identified the lactic acid method as the most effective in disrupting the cell walls of P. rhodozyma. The software, Design Expert, was used in the process of extracting astaxanthin from cell lysates using a subcritical extraction method. Through fitting analysis and response surface optimization analysis by Design Expert, the optimal extraction conditions were determined as follows: an extraction temperature of 41 °C, extraction frequency of two times, and extraction time of 46 min. These parameters facilitated the efficient extraction, concentration, and enrichment of astaxanthin from P. rhodozyma, resulting in an astaxanthin concentration of 540.00 mg/L. This result can establish the foundation for its high-value applications.