In this study, proteins were prepared from Schizochytrium pombe residue after oil extraction using isoelectric point precipitation, and their physicochemical and emulsifying properties were investigated. Our objective was to assess the suitability of these proteins for functional ingredient applications. Through a one-way experiment and optimization using response surface design, the effects of time, temperature, pH, and the material–liquid ratio of NaOH alkaline extraction were explored. The isoelectric point is verified by isoelectric point precipitation; the results revealed that crude protein from Schizochytrium (SCP) is minimally soluble at pH 4.2. Compared with whey protein (WP), it promotes better emulsion stability through the emulsification test. This study suggests that Schizochytrium oil-processing byproducts represent a promising source of protein, with potential applications as functional ingredients, offering implications for the usage of these byproducts in various industries.