The invention discloses an underwater tree safety system for deep water operating hydrate suppression. The underwater tree safety system comprises suppression agent injection pointswhich are arrangedbetween underwater trees at equal intervals in the underwater tree axis direction, first injecting valves which are arranged at the suppression agent injection points and are used for injecting a thermodynamics suppression agent, second injecting valves which are arranged at the suppression agent injection points and are used for injecting a dynamics suppression agent, winches which are connectedwith the underwater trees and are used for controlling the underwater trees to move in the axial direction of an underground tubular column to enable the suppression agent injection points to cover the whole underground tubular column. Multipoint monitoring to the underground tubular column is achieved, and efficient hydrate suppression is achieved. The invention further discloses an underwater tree safety suppression method for deep water operating hydrate suppression. Opening of the first injecting valves and the second injecting valves and addition depth of the suppression agent are determined based on a BP neural network, addition of the thermodynamics suppression agent and the dynamics suppression agent can be controlled, and hydrate formation can be effectively suppressed.