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Moon-based synthetic aperture radar (SAR) offers unprecedented temporal and spatial coverage. Its repeat-pass interferometry is expected to play a substantial role in earth science because of its large-scale, long-term, near 24.8 h revisit period, and stable earth observation ability. However, it faces a greater challenge when the signal passes through the ionosphere compared with the low Earth orbit (LEO) satellite. In this study, we constructed a total electron content (hereafter referred to as TEC) calculation model for the propagation path of a moon-based SAR signal based on International reference ionosphere model and moon-based SAR interferometry (InSAR) geometry. Subsequently, the ionospheric delay at various carrier frequencies was quantitatively evaluated under different time baseline types. The results show that the interferometric phase space gradient caused by ionospheric can reach ten times that of LEO SAR satellites with superposition of diurnal and seasonal ionospheric variations. In addition, this problem in the observation area with a large incident angle is more severe, which limits the effective swath width of moon-based repeat-pass InSAR. The ionospheric delay effects can be avoided to some extent by selecting the interference combination at nighttime or approaching the solar altitude angle. To highlight the large-scale ground deformation information in most cases and give full play to the long-term and stable observation advantages of the moon-based platform, accurate ionospheric correction or compensation must be considered.