The invention discloses a deepwater compound crossover pipe with flexible joints. The deepwater compound crossover pipe is provided with an M-shaped rigid crossover pipe; end vertical connectors are respectively arranged at the bottoms of two opposite vertical pipes of the M-shaped rigid crossover pipe; the flexible joints are respectively arranged on the two opposite vertical pipes, and are respectively provided with locking mechanisms; and lifting rings are respectively mounted on two high ends of the M-shaped rigid crossover pipe. The compound crossover pipe can effectively reduce or eliminate the pipe stress, in particular the pipe terminal connector load caused by the measurement installation errors and the design allowances in the crossover pipe design manufacturing and installation process, solves the problems of deformation or even break of the crossover pipe caused by excessive stress and the end connector failure, the service life of the crossover pipe is prolonged, and the end connection safety and reliability is guaranteed.