We investigate the nature of the topological quantum phase transition between the gapless and gapped Kitaev quantum spin liquid phases away from the exactly solvable point. The transition is driven by anisotropy of the Kitaev couplings. At the critical point, the two Dirac points of the gapless Majorana modes merge, resulting in the formation of a semi-Dirac point with quadratic and linear band touching directions. We derive an effective Gross-Neveu-Yukawa-type field theory that describes the topological phase transition in the presence of additional magnetic interactions. We obtain the infrared scaling form of the propagator of the dynamical Ising order parameter field and perform a renormalization-group analysis. The universality of the transition is found to be different from that of symmetry-breaking phase transitions of semi-Dirac electrons. However, as in the electronic case, the Majorana fermions acquire an anomalous dimension, indicative of the breakdown of the fractionalized quasiparticle description.