Emulsion gels with denser network microstructure and stronger mechanical properties have attracted increasing attentions for delivering lipophilic compounds. In this study, the effect of three distinct soluble dietary fiber (inulin (IN), resistant dextrin (RD) and stachyose (ST)) on the rheological, mechanical and microstructural properties of soy protein isolate (SPI) emulsion gel were firstly investigated. Compared with RD and IN, ST significantly accelerated water holding capacity and thermal stability, which exhibited more compact microstructure and more uniform emulsified oil droplets. Subsequently, the stability and bioavailability of vitamin D3 (VD3) in different delivery systems (medium chain triglycerides (MCT) embedding, SPI-ST emulsion embedding, SPI emulsion gel embedding and SPI-ST emulsion gel embedding) were continue evaluated. In vitro simulated digestion experiment demonstrated that the bioaccessibility of encapsulated VD3 in SPI-ST emulsion gel (69.95 %) was much higher than that of free embedding (48.99 %). In vivo pharmacokinetic experiment revealed that the bioavailability of VD3 was significantly enhanced in SPI-ST gel (p < 0.05), with the AUC0-24h value of 25-OH VD3 (the main circulating form of VD3) were 1.34-fold, 1.23-fold higher than that of free embedding, MCT embedding, respectively. These findings provide a possible approach for the development of high protein/fiber functional foods containing enhanced hydrophobic bioactives.