This study investigated how different extraction parts of raw materials and different flocculation methods affect the extraction yield, structure, and properties of sodium alginate. The aim was to improve the quality of sodium alginate and provide theoretical guidance for upstream enterprises. In this study, Lessonia nigrescens (LN) was used as a raw material. The alkali treatment conditions were optimized. The optimal extraction conditions were determined to be a 2% sodium carbonate concentration, a duration of 4 h, a material-to-liquid ratio of 1:40, and a temperature of 60 °C, achieving an extraction yield of 43.03%. LN was categorized into blades, stipes, holdfasts, and whole seaweed for comparative analysis, and sodium alginate was flocculated using the acid, calcium, and ethanol methods. Structural and physicochemical analyses showed that the mannuronic acid/guluronic acid (M/G) ratios of the twelve sodium alginate samples ranged from 5.73 to 8.76. The LN part had a greater influence on the M/G ratio than the flocculation method. The relative molecular weight (2343–3074 kDa) and viscosity (170–331 mPa·s) exhibited consistent trends. For the same part, the effect of the flocculation method on the molecular weight followed the order ethanol > acid > calcium. The physicochemical properties of the extracted sodium alginate met the requirements specified in the physicochemical index standard GB 1886.243-2016 of China.