The present invention provides a real time nucleic acid amplification reaction method comprising performing a nucleic acid amplification reaction in a droplet present in a container. The droplet is composed of a nucleic acid amplification reaction liquid including a nucleic acid to be amplified and magnetic particles. The container holds a droplet encapsulating medium immiscible with the nucleic acid amplification reaction liquid forming the droplet, and has a transport surface having a temperature gradient. Fluorochrome is initially contained in the droplet encapsulating medium, and optionally in the droplet, at start of the nucleic acid amplification reaction. The droplet is transported together with the magnetic particles by generating and applying a magnetic field so that the droplet is placed on the transport surface at a temperature point at which the nucleic acid synthesis reaction is started and maintained, thereby controlling a temperature of the reaction liquid.