The invention discloses a comprehensive construction method of subarea subsection water stoppage of an urban deep tunnel. The method involves an ordinary section, a special water-rich section and a transition section; for the special water-rich section, lining pipe pieces are divided into subareas according to rings, and two rings at the two ends are taken as chemical slurry blocking rings; annular gaps between the rest of lining pipe pieces and a stratum are filled with ordinary mortar, and cement paste backfilling is performed after the construction of the chemical slurry blocking rings is completed; the construction mode through cement paste backfilling is adopted for ordinary mortar, line-by-line grouting is carried out on all the lining pipe pieces between two blocking rings in each subarea in the sequence of bottom to middle to top, and the retreating type grouting sequence opposite to the excavating direction is adopted for each line. By means of the innovative combined type subsection subarea water stoppage mode, the tunnel construction quality and progress are ensured, and the problems that a surrounding hydrological environment is affected by tunnel construction and waterseepage and water leakage happen to a tunnel body after construction are effectively solved.