The invention discloses a waveguide invariant estimation method based on a deep sea vertical array, which relates to the technical field of underwater acoustic parameter estimation, can estimate waveguide invariants under two conditions of known and unknown target distances, and is simple and convenient. The waveguide invariant estimation method is characterized by comprising the following steps of: S1, establishing a function relationship among a waveguide invariant beta, a multipath time delay parameter bv, a signal arrival glancing angle theta, an arrival time delay t and a target distance R; S2, utilizing a target radiation sound signal received by a vertical hydrophone array deployed at a deep sea bottom, and carrying out short-time frequency domain beam forming processing on the target radiation sound signal to obtain a beam time delay diagram; S3, carrying out clustering on the wave beam time delay diagram and extracting a wave beam peak point and a corresponding time delay value; S4, carrying out curve fitting by using a least square method aiming at the head of the extracted wave beam peak so as to solve multipath time delay parameters; and S5, aiming at different target distance prior information, combining actual measurement multipath time delay parameters to estimate waveguide invariants.