To enhance Lactobacillus paracei F50 viability during spray drying and long-term storage, this study evaluates whey protein (WP) crosslinked with four polysaccharides (κ-carrageenan (KC), xanthan gum (XG), low-methoxyl pectin (LMP), sodium alginate (SA)) for the first time as protective matrices for L. paracasei F50 during spray drying. The four kinds of crosslinked wall materials were compared by various characterization methods. Among them, the WP-κ-carrageenan (WP-KC) composite exhibited optimal performance, forming a uniform microcapsule with high colloidal stability. After spray drying, WP-KC achieved the highest viable cell density (9.62 lg CFU/g) and survival rate (91.85%). Notably, WP-KC maintained viability above 8.68 lg CFU/g after 120 days of storage at 4 °C, surpassing other formulations. Structural analysis showed that the WP-KC microcapsule was completely encapsulated without breaking or leaking and confirmed the molecular interaction between WP and KC. Under the condition of high temperatures (≤142.63 °C), the wall material of the microcapsule does not undergo any endothermic or exothermic process and is in a state of thermodynamic equilibrium, with excellent stability and good dispersion. Additionally, microcapsules exhibited enhanced resistance to thermal stress (55–75 °C) and UV irradiation, higher than that of free cells. These results highlight WP-KC as an industrially viable encapsulation system for improving probiotic stability in functional foods, offering critical insights into polysaccharide–protein interactions for optimized delivery systems.