Quality of Experience assessment in stereoscopic 3D is a challenging topic and existing standards such as ITU-R BT.500 may no longer be appropriate. The paper presents a new methodology for 3D video subjective quality evaluation. The novel method was developed to compare different multi-view video compression technologies. A time-efficient solution was proposed as a multi stimulus plus simultaneous presentation extension of the conventional DSCQS method. Experimental results conducted on an auto stereoscopic display for H.264 and H.265 based encoders are also provided. The results demonstrate that the new methodology is superior to the DSCQS method in terms of both evaluation time and accuracy.