Relatively high heat input and heat accumulation are treated as critical challenges to affect the qualities and performances of components fabricated by wire arc additive manufacturing (WAAM). In this study, various heat inputs, namely 276, 552 and 828 J/mm, were performed to fabricate three thin-wall Inconel 625 structures by cold metal transfer (CMT)-based WAAM, respec-tively, and active interpass cooling was conducted to limit heat accumulation. The macrostructure, microstructure and mechanical properties of the produced components by CMT were investigated. It was found that the increased heat input can deteriorate surface roughness, and the size of dendrite arm spacing increases with increasing heat input, thus leading to the deterioration of mechanical properties. Lower heat input and application of active interpass cooling can be an effective method to refine microstructure and reduce anisotropy. This study enhances the understanding of interpass temperature control and the effectiveness of heat inputs for Inconel 625 alloy by WAAM. It also provides a valuable in situ process for microstructure and mechanical properties’ refinement of WAAM-fabricated alloys and the control of heat accumulation for the fabrication of large-sized structures for future practical applications.