What is believed to be a new analysis algorithm to carry out profile measurement with low computational complexity and less noise sensitivity is presented. First, a discrete cosine transform (DCT)-based representation method is introduced to express the height distribution of a 3D surface. Then a novel shift estimation algorithm, called the DCT-based shift estimation (DCT-SE), is presented to reconstruct 3D object surfaces by using the proposed expression and the generalized analysis model. The advantage of DCT-SE is that without loss of measurement precision it provides lower computational complexity to implement 3D reconstruction from nonlinearly distorted fringe patterns and, at the same time, survives the random noise. Simulations and experiments show that the proposed DCT-SE is a fast, accurate, and efficient reconstruction algorithm for digital projection- based fringe pattern profilometry techniques.