Generally, the topological corner state in two-dimensional second-order topological insulator (2D SOTI) is equivalent to the well-known domain wall state, originated from the mass-inversion between two adjacent edges with phase shift of π. In this work, go beyond this conventional physical picture, we report a fractional mass-kink induced 2D SOTI in monolayer FeSe with canted checkerboard antiferromagnetic (AFM) order by analytic model and first-principles calculations. The canted spin associated in-plane Zeeman field can gap out the quantum spin Hall edge state of FeSe, forming a fractional mass-kink with phase shift of π/2 at the rectangular corner, and generating an in-gap topological corner state with fractional charge of e/4. Moreover, the topological corner state is robust to local perturbation, existing in both naturally and non-naturally cleaved corners, regardless of the edge orientation. Our results not only demonstrate a material system to realize the unique 2D AFM SOTI, but also pave a new way to design the higher-order topological states from fractional mass-kink with arbitrary phase shift, which are expected to draw immediate experimental attention.