Shrinkage during hardening and curing is one of the largest challenges for the widespread application of metakaolin-based geopolymers (MKGs). To solve this problem, a silane coupling agent (SCA) and waterborne epoxy resin (WER) were used to synthesize MKG composites. The individual and synergistic effects of the SCA and WER on chemical, autogenous, and drying shrinkage were assessed, the modification mechanisms were investigated by microstructural characterization, and shrinkage resistance was evaluated by the chloride ion permeability of MKG composite coatings. The results showed that the SCA and WER significantly decreased the chemical shrinkage, autogenous shrinkage, and drying shrinkage of the MKG, with the highest reductions of 46.4%, 131.2%, and 25.2% obtained by the combination of 20 wt% WER and 1 wt% SCA. The incorporation of the organic modifiers densified the microstructure. Compared with the MKG, the total volume of mesopores and macropores in MKG-WER, MKG-SCA, and MKG-WER-SCA decreased by 11.5%, 8.7%, and 3.8%, respectively. In particular, the silanol hydrolyzed from the SCA can react with the opened epoxy ring of the WER and the aluminosilicate oligomers simultaneously to form a compact network and resist shrinkage during the hardening and continuous reaction of the geopolymer. Furthermore, the apparently lowered chloride ion diffusion coefficient of concrete (i.e., reduction of 51.4% to 59.5%) by the WER- and SCA-modified MKG coatings verified their improved shrinkage resistance. The findings in this study provide promising methods to essentially solve the shrinkage problem of MKGs at the microscale and shed light on the modification mechanism by WERs and SCAs, and they also suggest the applicability of MKG composites in protective coatings for marine concrete.