The influence of heat input in electron beam (EB) process on microstructure, mechanical properties, and pitting corrosion resistance of duplex stainless steel (DSS) welded interface was investigated. The rapid cooling in EB welding resulted in insufficient austenite formation. The austenite mainly consisted of grain boundary austenite and intragranular austenite, and there was abundant Cr2N precipitation in the ferrite. The Ni, Mo, and Si segregation indicated that the dendritic solidification was primarily ferrite in the weld. The weld exhibited higher hardness, lower toughness, and poorer pitting corrosion resistance than the base metal. The impact fractures of the welds were dominated by the transgranular cleavage failure of the ferrite. The ferrite was selectively attacked because of its lower pitting resistance equivalent number than that of austenite. The Cr2N precipitation accelerated the pitting corrosion. In summary, the optimised heat input slightly increased the austenite content, reduced the segregation degree and ferrite texture intensity, decreased the hardness, and improved the toughness and pitting corrosion resistance. However, the effects were limited. Furthermore, optimising the heat input could not suppress the Cr2N precipitation. Taking into full consideration the microstructure and properties, a heat input of 0.46 kJ/mm is recommended for the EB welding of DSS.