Although graphene oxide lamellar membranes (GOLMs) are effective in blocking large organic molecules and nanoparticles for nanofiltration and ultrafiltration, water desalination with GOLM is challenging, with seriously controversial results. Here, a combined experimental and molecular dynamics simulation study shows that intrinsic high water/ion selectivity of GOLM was achieved in concentration gradient-driven diffusion, showing great promise in water desalination. However, in pressure-driven filtration the salt rejection was poor. This study unveils a long-overlooked reason behind the controversy in water desalination with GOLM and further provides a fundamental understanding on the in-depth mechanism concerning the strong correlation of water/ion selectivity with the applied pressure and GO nanochannel length. Our calculations and experiments show that the applied pressure weakened the water-ion interactions in GO nanochannels and reduced their permeation selectivity, while the length of nanochannels dominated the mass transport processes and the ion selectivity. The new insights presented here may open up new opportunities for the optimization of GOLMs in this challenging area.