The invention belongs to the technical field of privacy protection, and discloses a big data based position privacy protection system with a homomorphic encryption mechanism. The big data based position privacy protection system with the homomorphic encryption mechanism comprises a positioning module, a data transmission module, a central processing module, an encryption module, a data storage module, a position inquiry module and a display module. According to the invention, by the encryption module, in the same environment configuration, compared to the bootstrap process in an original scheme, the bootstrap process is reduced by 47%; safety of the scheme can be specified to the LWE problem, and can reach safety of 128 bits; and meanwhile, according to the invention, a cloud server and ahomomorphic encryption algorithm are introduced by the position inquiry module, a user can obtain a corresponding inquiry result only by implementing homomorphic encryption for once, homomorphic multiplication for once and subtraction operation for once, so that calculation cost of the user is reduced.