To reduce the efflorescence extent of metakaolin (MK)-based geopolymer, this study introduced thermally activated modified calcium montmorillonite (MT) and 5 A zeolite (ZT) into MK-based geopolymer, and the optimal mixing ratio was acquired by response surface methodology. The effect of the two modified clay minerals on the microstructural and mechanical properties of the MT-ZT-MK geopolymer was explored by compressive strength testing, phase analysis (XRD and FTIR), pore structure analysis (MIP), and morphology analysis (SEM-EDS). To investigate the performance and mechanism of efflorescence inhibition of the ternary geopolymer, the cation concentration in the leaching solution was detected by inductively coupled plasma atomic emission spectrometry (ICP-OES), and the efflorescence area of the geopolymer was calculated using Image Pro Plus (IPP) software. The results of the experiment showed that the optimal mixing ratio, as determined by RSM, was 1.5 wt% of modified MT and 2.9 wt% of modified ZT, with the highest compressive strength at 65.1 MPa and the lowest degree of efflorescence after 28 days of curing. It can be concluded that the two clays gradually exhibit the effect of cation exchange and internal curing. The pore structure is optimized and (N, C)-A-S-H gels are formed with the extension of curing time. On the other hand, the lesser extent of efflorescence possibly is attributed to the restricted channels for Na+ in the matrix to undergo carbonation with CO2 in the air.