We calculate the gravitational wave (GW) background spectrum from kink-kink collisions on infinite cosmic strings by taking into account the effect of Y-junctions. A kink going through a Y-junction transforms into three daughter kinks. In this way, the existence of Y-junctions also increases the number of kinks on cosmic strings with Y-junctions. However, at the same time, it smooths out the sharpness of kinks rapidly and reduces the number of sharp kinks, which are responsible for the emissions of strong GW bursts. We compute the number distribution of kinks as a function of the sharpness by taking into account the effect of Y-junctions and translate it to the amplitude of the GW background spectra. We first investigate the case of the string network with equal string tensions and find that the effect of Y-junctions to smooth out kink sharpness dominates that of the enhancement of the kink number by a small reconnection probability, and the GW amplitude turns out to be smaller than the ordinary cosmic string case. On the other hand, for non-equal string tensions, we find that the GW spectrum does not change significantly compared to the equal-tension case.