I present our result on constraining the reionization history using Lyman alpha emitting galaxies. Our method combines the Subaru LAE survey result with cosmological hydrodynamical, radiative transfer simulations of reionization which capture the effect of both the large-scale bubble morphology and small-scale neutral gas. We find that the current observation favours a large neutral fraction of the IGM at z~7 of >10%, although the uncertainty from the small-scale neutral gas can relax the constraint to >1%. I also discuss our new theoretical result on combining both Lyman alpha in emission and absorption to probe the CGM of the high-redshift Lyman alpha emitting galaxies. Using the new technique using both Lyman alpha in emission and absorption together, I argue that Subaru/HSC survey can constrain both the history and morphology/topology of reionization.