Gold-silver (Au@Ag) core-shell nanostructures have a stronger surface plasma response, wider absorption and scattering in the UV-vis-NIR region, and distinctive optical properties, which are widely explored in biosensors, information processing, photothermal therapy, and catalysis. Core-shell nanostructures are usually formed by the deposition of the second metal atoms onto the first core metal particles via the chemical wet method. The conventional approaches for the manipulation of the shape usually were done by homogeneous growth or etching of isotropic nanoparticles. Through in situ modification of the first metal core at the different locations, the different growth model of the second metal can be regulated to control the shapes of core-shell structures. Herein, we modified the gold nanorods (AuNRs) asymmetrically at the end and side parts using thiolated molecules to regulate the morphology of gold nanorod@silver (AuNR@Ag) core-shell nanoparticles. Interestingly, the obvious eccentric nanostructures of AuNR@Ag core-shell nanoparticles were obtained with the increase of the molecular weight of macromolecules modified at the end of AuNRs. Therefore the growth mode was adjusted from Frank-van der Merwe mode to Stranski-Krastanow mode. By changing the length of the hydrocarbon chain and functional groups of the small mercaptan molecules at the side of AuNRs, the silver shell exhibits selective growth at the side of the AuNRs, resulting in heterogeneous core-shell nanoparticles and various shapes of the AuNR@Ag core-shell. Our method opens up a new avenue toward preparing core shell nanostructures with controlled shapes, and the obtained structures are promising in various applications.