The present disclosure provides a semiconductor structure, including a transistor layer, a memory region over the transistor layer, and a logic region adjacent to the memory region. The memory region includes a first Nth metal line, a magnetic tunneling junction (MTJ) over the first Nth metal line, a cap over the MTJ, a first stop layer on the cap; and a first (N+1)th metal via over the MTJ. The first (N+1)th metal via is laterally surrounded by the cap and the first stop layer. The logic region includes a second Nth metal line, a second stop layer being disposed over an (N+1)th metal line, and a second (N+1)th metal via over the (N+1)th metal line. N is an integer greater than or equal to 1. A method of manufacturing the semiconductor structure is also disclosed.