Systems, methods, and apparatus for determining permeability of subsurface formations are provided. In one aspect, a method includes: positioning a sample of the subsurface formation in a measurement cell, fluidly connecting an inlet and an outlet of the sample to an upstream reservoir and a downstream reservoir, respectively, flowing a fluid through the sample from the upstream reservoir to the downstream reservoir, measuring changes of an upstream pressure associated with the upstream reservoir and a downstream pressure associated with the downstream reservoir in a measurement time period, and determining a matrix permeability of the subsurface formation based on measurement data before the upstream pressure and the downstream pressure merge at a merging time point.