The soft gluon resummation effect in the Higgs boson plus two-jet production at the LHC is studied by applying the transverse momentum dependent factorization formalism. The large logarithms, introduced by the small total transverse momentum of the Higgs boson plus two-jet final state system, are resummed to all orders in the expansion of the strong interaction coupling with the accuracy of Next-to-Leading Logarithm order. This significantly improves the theoretical prediction. We also compare our result with the prediction of the Monte Carlo event generator Pythia8, and find noticeable difference in the distributions of the total transverse momentum and the azimuthal angle correlations of the final state Higgs boson and two-jet system, when applying similar kinematic cuts used in the LHC data analysis. This difference is large enough to affect the measurement of Higgs boson coupling to the vector boson at the future High luminosity LHC.