Disclosed are a system and a method for monitoring unsaturated zone gas and near-surface atmosphere in real time by using an isotope analyzer. The system includes a near-surface atmosphere analyzer including a fixing member, a plurality of near-surface gas inlets, a plurality of gas transfer members communicating with the near-surface gas inlets, an analyzing member including an isotope analyzer, which analyzes an isotope of gas transferred through the gas transfer members, a channel connected to the gas transfer members and the analyzing member to select one gas transfer member and to supply gas transferred through the selected gas transfer member to the analyzing member, and a connection member connecting the channel to the analyzing member, a communication device transmitting components of the isotope output from the isotope analyzer, and a monitoring server outputting the components of the isotope transmitted from the communication device.