This study presented a convenient method of gathering, splitting, merging, and sorting microdroplets by dynamic pneumatic rails in double-layered microfluidic devices. In these devices, the pneumatic rails were placed below the droplet channel, with a thin elastic polydimethylsiloxane (PDMS) film between them. The PDMS film would sag down to the rail channel, forming a groove pattern at the bottom of the droplet channel, when the fluid pressure in the droplet channel was higher than the air pressure in the rail channel. The groove could capture the flattened droplets and guide the flow path of them due to the lowered surface energy when they extended into the groove. We have designed different components consisting of pneumatic rails to split, merge and sort droplets, and demonstrated that the components maintained good performance in manipulating droplets only by controlling the air pressure. Furthermore, a pneumatic rail-based sorter has been successfully used to sort out single-cell droplets. The pneumatic rail can be integrated into pneumatic valve-based microfluidic devices to be a flexible tool for droplet-based biological and chemical analysis.