A recent experiment shows surprising glass-like features [npj Quantum Materials 6, 1 (2021)] in the nearly disorder-free α-RuCl3, a Kitaev spin liquid candidate, at low temperatures in the intermediate magnetic field region. Inspired by this experiment, we study the Kitaev model within the density-matrix renormalization group (DMRG) method in the presence of a magnetic field at zero temperature. We find five distinct phases with increasing magnetic field, which are characterized by a homogeneous flux phase, the Z2 vortex gas, solid and emergent glass phase in the so-called U (1) spin liquid region, and finally a spin-polarized phase. The emergent glassiness is confirmed by calculating correlation functions as well as ground state fidelity, showing a plethora of energetically accessible orthogonal saddle points corresponding to different flux configurations. Taking our result together with previous theories of emergent glassiness in disorder-free quantum many-body systems, we propose that glassiness is intrinsic to disorder-free generic quantum spin liquids.