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Abstract We study the effect of D-instantons on closed string scattering amplitudes in the two-dimensional type 0B string theory from the worldsheet perspective. We find that the contribution from a pair of D-instanton and anti-D-instanton to the closed string reflection amplitude, with a suitable contour prescription for the integration over the D-instanton moduli space, agrees with the corresponding leading non-perturbative corrections in the proposed dual matrix quantum mechanics. This analysis is further extended to thermal observables defined at finite temperature. The infrared divergence in charged processes is understood through the measure factor for charged D-instantons, and can be treated with spacetime dimensional regularization.