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Polysaccharides, which can be affected by different preparations, play a crucial role in the biological function of Paecilomyces hepiali (PHPS) as a health food. To explore high-valued polysaccharides and reduce the negative influence of human involvement, a green tailorable deep eutectic solvent (DES) was applied to optimize the extraction of polysaccharides (PHPS-D), followed by the evaluation of the structural properties and immunomodulation by comparison with the hot-water method (PHPS-W). The results indicated that the best system for PHPS-D was a type of carboxylic acid-based DES consisting of choline chloride and succinic acid in the molar ratio of 1:3, with a 30% water content. The optimal condition was as follows: liquid–solid ratio of 50 mL/g, extraction temperature of 85 °C, and extraction time of 1.7 h. The actual PHPS-D yield was 12.78 ± 0.17%, which was obviously higher than that of PHPS-W. The structural characteristics suggested that PHPS-D contained more uronic acid (22.34 ± 1.38%) and glucose (40.3 ± 0.5%), with a higher molecular weight (3.26 × 105 g/mol) and longer radius of gyration (78.2 ± 3.6 nm), as well as extended chain conformation, compared with PHPS-W, and these results were confirmed by AFM and SEM. Immunomodulatory assays suggested that PHPS-D showed better performance than PHPS-W regarding pinocytic activity and the secretion of NO and pro-inflammatory cytokines (IL-6, TNF-α and IL-1β) by activating the corresponding mRNA expression in RAW264.7 cells. This study showed that carboxylic acid-based DES could be a promising tailorable green system for acidic polysaccharide preparation and the valorization of P. hepiali in functional foods.