Cadmium (Cd) contamination of wheat fields is a major environmental problem. Sulfhydryl-grafted palygorskite (SGP) has been used as an efficient amendment to immobilize Cd in calcareous wheat fields. However, information on the long-term effects of SGP on soil Cd immobilization and accumulation in wheat remains limited. In this study, wheat pot and freeze–thaw (F/T) cycle experiments were conducted to explore the remediation stability of SGP during winter wheat growing. The wheat pot experiments showed that applying 0.1–0.2%SGP significantly decreased Cd in wheat grains by 21.57–57.85% in the second year. The application of 0.2%SGP decreased diethylenetriaminepentaacetic acid (DTPA) extractable Cd by 33.84–39.70%, increased DTPA extractable Mn by 11.22–15.86%, and promoted the conversion of exchangeable Cd into carbonate-bound and Fe/Mn oxide-bound Cd fractions in the soil in the second year. The composition and function of soil bacteria differed under the SGP treatment for two consecutive years. F/T cycle experiments showed that F/T cycles did not affect soil pH but converted exchangeable Cd and carbonate-bound Cd to the residual Cd fraction (6%) and increased the mass fraction of > 2 mm soil aggregates. Under 0.2%SGP application, F/T cycles further decreased the available soil Cd concentration and increased the immobilization efficiency of SGP on Cd by 9.37–11.82% in various aggregates. Although SGP can reduce Cd accumulation in wheat for two consecutive years, the remediation efficiency decreased compared to that in the first year, which is unrelated to seasonal F/T cycles; the specific reasons for this reduction must be further explored. Overall, SGP displayed long-term immobilization effects on Cd in wheat fields and showed higher efficiency under F/T cycle conditions, with the potential for long-term remediation of Cd-contaminated calcareous soils in cold regions.