A simple aspheric chromatic dispersion lens group of low cost is designed using Zemax, and an integrated fiber-coupled chromatic confocal 3D measurement system is developed. Performances of four peak wavelength extraction methods, i.e. the maximum method, centroid method, Gaussian fitting method and spline interpolation method, have been compared and analyzed quantitatively. In addition, calibration accuracy of Gaussian fitting method and spline interpolation method is tested and compared through the axial resolution and displacement measurement experiments. The experimental results show that the axial measurement range of the built system is 1 mm. The Gaussian fitting method has higher accuracy and better stability among the four peak extraction algorithms. The axial resolution of the system using Gaussian fitting based and spline interpolation based calibration methods can both reach 0.2 μm and the displacement measurement accuracy is better than 1% within the whole measurement range; a quartz glass with a thickness of 0.219 mm is measured, and the relative measurement error of the average value is 0.5%. Finally, the developed system is applied to the 3D surface measurement of a step structure, a flexible electrode and a MEMS unit, and the experimental results indicate that the proposed system can perform high-precision 3D measurements of complex microstructures and transparent material thicknesses.