This paper presents a novel non-destructive testing system, magneto-eddy current sensor (MECS), to enable surface profiling of dissimilar materials by combining magnetic sensing for ferromagnetic materials and eddy current sensing for non-ferromagnetic materials. The interactions between an electromagnetic field and non-ferromagnetic surface and between a magnetic field and ferromagnetic surface were measured by MECS. The MECS consists of a conic neodymium magnet and a copper coil wound around the magnet. Aluminum and steel surfaces bonded together were prepared to test non-destructive surface profiling of dissimilar materials by MECS. The interactions between an electromagnetic field and aluminum surface were characterized by monitoring the impedance of the coil, and the interactions between a magnetic field and steel surface were characterized by using a force sensor attached to the neodymium magnet. The magnetic and electromagnetic effects were numerically analyzed by finite element model. The developed MECS showed the following performance: measurement spot size 5 mm and 10mm, dynamic measurement bandwidth 15 kHz and 10 kHz, measuring range 25 mm and 17 mm, polynomial fitting error 0.51% and 0.50%, and resolution 0.655 μm and 0.782 μm for nonferromagnetic and ferromagnetic surface profiling, respectively. This technique was also applied to surface profiling and inspection of the rivet joining sheet materials. The results showed the MECS is capable of non-destructively monitoring and determining the riveting quality in a fast, large-area, low-cost, convenient manner.