Mastery over the structures at nano/microscale can effectively tailor the catalytic activity and durability of materials. Herein, three dimension (3D) hierarchical iron diselenide (FeSe2) microspheres have been successfully synthesized via a hot-injection method. The morphologies of building blocks and final products can be simply controlled by the amount and/or the type of alkythiols, from irregular micro/nanoparticles to uniform 3D hierarchical microspheres made of ultrathin nanosheets or rhombus-like nanorods. A formation mechanism has been understood based on the inherent crystal structure of FeSe2 and the selective adsorption of alkythiols. The as-obtained FeSe2 samples were employed as counter electrode (CE) materials in dye-sensitized solar cells (DSSCs). Electrochemical characterizations indicated that the 3D hierarchical FeSe2 microspheres composed of ultrathin nanosheets (FeSe2 NSs) exhibited low charge transfer resistance at the electrolyte–electrode interface, high electrocatalytic activity and fast reaction kinetics for the I−/I3 − redox reaction. A DSSC with FeSe2 NSs CE achieved a high power conversion efficiency of 8.39% under a simulated solar illumination of 100mWcm−2 (AM 1.5), comparable to that of Pt based devices (8.20%). Moreover, the fast activity onset and relatively long stability demonstrated that the FeSe2 NSs is a promising alternative to Pt in DSSC.