The high-resolution and nondestructive co-reference measurement of the inner and outer three-dimensional (3D) surface profiles of laser fusion targets is difficult to achieve. In this study, we propose a laser differential confocal (LDC)-atomic force probe (AFP) method to measure the inner and outer 3D surface profiles of laser fusion targets at a high resolution. This method utilizes the LDC method to detect the deflection of the AFP and exploits the high spatial resolution of the AFP to enhance the spatial resolution of the outer profile measurement. Nondestructive and co-reference measurements of the inner profile of a target were achieved using the tomographic characteristics of the LDC method. Furthermore, by combining multiple repositionings of the target using a horizontal slewing shaft, the inner and outer 3D surface profiles of the target were obtained, along with a power spectrum assessment of the entire surface. The experimental results revealed that the respective axial and lateral resolutions of the outer profile measurement were 0.5 and 1.3 nm, while the respective axial and lateral resolutions of the inner profile measurement were 2.0 nm and approximately 400.0 nm. The repeatabilities of the root-mean-square deviation measurements for the outer and inner profiles of the target were 2.6 and 2.4 nm, respectively. We believe our study provides a promising method for the high-resolution and nondestructive co-reference measurement of the inner and outer 3D profiles of laser fusion targets.