Haematococcus pluvialis accumulates astaxanthin, which is a high-value antioxidant, during the red cyst stage of its lifecycle. The development of a rigid cell wall in the cysts hinders the recovery of astaxanthin. We investigated morphological changes and cell disruption of mature H. pluvialis cyst cells while using high-pressure homogenization for astaxanthin extraction. When treated with French-press-cell (pressure, 10,000–30,000 psi; passage, 1–3), the intact cyst cells were significantly broken or fully ruptured, releasing cytoplasmic components, thereby facilitating the separation of astaxanthin by ethyl acetate. Fluorescence microscopy observations using three different fluorescent dyes revealed that a greater degree of cell breakage caused greater external dispersion of astaxanthin, chlorophyll, lipids, proteins, and carbohydrates. The mechanical treatment resulted in a high cell disruption rate of up to 91% based on microscopic cell typing and Coulter methods. After the ethyl acetate extraction, the astaxanthin concentration significantly increased by 15.2 mg/L in proportion to the increase in cell disruption rate, which indicates that cell disruption is a critical factor for solvent-based astaxanthin recovery. Furthermore, this study recommends a synergistic combination of the fast instrumental particle-volume-distribution analysis and microscope-based morphologic phenotyping for the development of practical H. pluvialis biorefinery processes that co-produce various biological products, including lipids, proteins, carbohydrates, chlorophyll, and astaxanthin.