Soil saline–alkali stress is a major problem faced by global agriculture, and there is an urgent need to develop efficient amelioration strategies. While both probiotics and plant stress-resistant molecules play critical roles in the alleviation of crop stress, their efficient retention in crop rhizosphere regions remains a great challenge. In this study, the nanocarrier ZIF-8@SPBP@betaine (ZSBet) was constructed by introduction of the synthesized polysaccharide-binding protein (SPBP) and the stress-resistant molecule betaine to the metal–organic framework ZIF-8. During co-incubation, the probiotic Novosphingobium capsulatum and ZSBet efficiently bound together to form ZSBet + Novo co-assemblies, i.e., the integrated protein-ZIF-8-probiotic complexes mediated by polysaccharide-receptor recognition, which exhibited strong root-binding abilities. Microbiome analysis revealed that ZSBet + Novo reduced the α-diversity of rhizosphere bacteria and increased the absolute abundance of biofilm formation-related bacteria, e.g., Novosphingobium, Sphingobium, and Lactococcus. During wheat cultivation in saline–alkali soil, ZSBet + Novo reduced soil pH by 0.63 units, decreased soil salt content by 0.11 g/kg, and increased soil nutrient levels. Furthermore, the co-assembly enhanced the wheat grain number by 145.05% and reduced root malondialdehyde and proline contents by 42.00% and 39.13%, respectively. This study provides a new strategy for improving crop resistance under saline–alkali stress in combination with nanotechnology and synthetic biology.