A manufacturing method of a semiconductor device includes the following steps. A first inter-metal dielectric (IMD) layer is formed on a substrate. A cap layer is formed on the first IMD layer. A connection structure is formed on the substrate and penetrates the cap layer and the first IMD layer. A magnetic tunnel junction (MTJ) stack is formed on the connection structure and the cap layer. A patterning process is performed to the MTJ stack for forming a MTJ structure on the connection structure and removing the cap layer. A spacer is formed on a sidewall of the MTJ structure and a sidewall of the connection structure. A second IMD layer is formed on the first IMD layer and surrounds the MTJ structure. The dielectric constant of the first IMD layer is lower than the dielectric constant of the second IMD layer.