Ferritic/martensitic (F/M) heat-resistant steels are one of the most promising candidate materials applied in core fuel assemblies such as cladding and packaging in nuclear reactors, but their weldments with high performance especially the creep properties were difficult to obtain by conventional welding methods due to the formation of heat-affected zone (HAZ) and rapid dissolution of precipitates. Here we successfully averted the formation of HAZ by reducing the heat input during welding to improve the structure-property synergy of a 12Cr-F/M steel joint via a low-temperature friction stir welding (FSW) technology. Complex microstructure regions consisting of stirred zone (SZ), fine-grained HAZ and inter-critical HAZ were generated in the traditional FSW joint with a high heat input, while only SZ and thermo-mechanically affected zone were found in the low-temperature FSW joint with a peak temperature between the Ac3 and Ac1 temperature. Under dynamic recrystallization at the α+γ two-phase region, ultrafine ferrite and martensite were generated and large amounts of precipitates were retained, giving rise to the greatly improved microhardness and superior tensile strength and impact toughness on par with that of the base metal. This work recommends a feasible technique to produce high-performance heat-resistant steel joints for lengthening the service life of nuclear reactors.