Sodium alginate exhibits poor stability when applied as a single gel network, which undermines its efficacy in probiotic encapsulation and protection. This study aimed to incorporate alginate (Alg) with cyclodextrin to prepare a supramolecular hydrogel to enhance the encapsulation and viability of probiotics. Specifically, l-tryptophan (L-Trp) and Sulfobutylether-β-cyclodextrin (SBE-β-CD) were employed to self-assemble into an inclusion complex (IC). Alg/Trp-SBE-β-CD hydrogels were formed using calcium ion-mediated cross-linking and IC addition. Experimental data revealed that the Alg/Trp-SBE-β-CD gels with 1 wt% CaCl2 exhibited good overall performance. The hydrogels significantly improved the stability and release properties of loaded Bifidobacterium animalis F1-7 compared to single Alg gels. Notably, the survival rate was 95.5% after 2 h in simulated gastric fluid (SGF), and the release rate reached 97.7% after continuous release in simulated intestinal fluid (SIF) for 6 h. Probiotic viable counts were maintained at 7–8 log CFU/g after 4 weeks of storage. This study indicates that a hybrid wall material of Alg and Trp-SBE-β-CD IC can enhance the stability and controlled release of bioactive compounds including synbiotics (prebiotics + probiotic preparations).