We report an interesting magnetic behavior of a Co film (thickness ~ 350 {AA}) grown on Si/Ti/Cu buffer layer by electro-deposition (ED) technique. Using depth sensitive X-ray reflectivity and polarized neutron reflectivity (PNR) we observed two layer structures for the Co film grown by ED with a surface layer (thickness ~ 100 {AA}) of reduced density (~ 68% of bulk) compared to rest of the Co film (thickness ~ 250 {AA}). The two layer structure is consistent with the histogram profile obtained from atomic force microscope (AFM) of the film. Interestingly, using PNR, we found that the magnetization in the surface Co layer is inversely (antiferomagnetically) coupled (negative magnetization for surface Co layer) with the rest of the Co layer for the ED grown film. While we compare PNR result for a Co film of similar layered structure grown by sputtering, the film showed a uniform magnetization as expected. We also show that the depth dependent unusual magnetic behavior of ED grown Co film may be responsible for anomalous anisotropic magnetoresistance observed in low field in this film as compared to the Co film grown by sputtering. Combining X-ray scattering, AFM, superconducting quantum interface device magnetometry (SQUID), PNR and magneto-transport measurements we attempted to correlate and compare the structural, magnetic and morphological properties with magneto-transport of Co films grown by ED and sputtering. The study indicates that the interesting surface magnetic property and magneto-transport property of the ED film is caused by its unique surface morphology.