High-strength steels are essential materials in various sectors, such as engineering machinery, marine engineering, and hydropower. Welding is a crucial thermal processing technique for fabricating structural components made of high-strength steels. The weld metal, as a vital component of the welded joint, plays a pivotal role in determining the applicability and service life of weldments through its microstructural characteristics and properties. At present, steel manufacturers globally have developed 1000 MPa grade high-strength steels. However, the welding consumables associated with these steels exhibit inadequate strength-toughness matching, which significantly hinders their widespread adoption. In this study, weld metals of 1000 MPa grade high-strength steels with three different Mo contents were produced via the gas metal arc welding process. A comprehensive investigation of the microstructure and mechanical properties of weld metals of 1000 MPa grade high-strength steels were conducted using SEM, EBSD, TEM, tensile testing, and Charpy impact testing. The influence mechanism of Mo content on the microstructural evolution was elucidated. The microstructural characterization revealed that the weld metals predominantly comprised lath bainite (LB) and coalesced bainite (CB). As the Mo content was increased, the proportion of high angle grain boundaries initially decreased and then increased. The morphology of LB transitioned from an interwoven structure to a more parallel arrangement, which was accompanied by an increase in the CB content. Mechanical testing revealed that a higher Mo content enhanced the metal hardenability, resulting in increased yield strength, tensile strength, and hardness. In contrast, the impact toughness initially decreased and then slightly increased. Analysis of the crack propagation paths on the cross-sections beneath the impact fracture surfaces demonstrated that the cracks readily propagated through the CB regions. The presence of CB considerably impaired the impact toughness of the weld metals. The optimal balance between strength and toughness in the weld metals was achieved at 0.71% Mo, resulting in a yield strength of (939 ± 10) MPa, a tensile strength of (1181 ± 2) MPa, and a room-temperature impact energy of (60 ± 3) J.