A method and system for measuring deep trench structures of dynamic random access memory (DRAM) based on Fourier transform infrared (FTIR) reflectometry is proposed. The principle of the measurement system is presented, along with a detailed description of the optical path design. By regulating the slit aperture to decrease the size of the detection spot and optimizing the incidence angle onto the wafer, the reflection from the backside of the wafer is suppressed, thus the signal-to-noise ratio (SNR) of the measurement is increased significantly. The experiments carried out on the deep trench structures of DRAM demonstrate that the trench geometric parameters can be extracted with a nanometer scale accuracy using the proposed system, thus the technique is proven to provide a non-contact, nondestructive, time-effective, low-cost and high resolution tool for the measurement of deep trench structures. It is expected that the proposed technique will find potential applications in the on-line monitoring and process control for microelectronics and microelectromechanical system (MEMS) manufacturing.