The invention discloses an inner detection system for submarine pipelines and a detection method thereof. The inner detection system comprises an electronic sealed cabin arranged in a supporting frame. The supporting frame is provided with a supporting roller array, an odometer wheel, a pressure sensor, a temperature sensor and a sound sensor, wherein the supporting roller array, the odometer wheel, the pressure sensor, the temperature sensor and the sound sensor are distributed in an annular mode. The detection method includes: the inner detection system is connected to an upper computer to download signals collected by the sensors, and filtering and noise reduction processing is performed on the signals; traveling mileage of the inner detection system and included angles of the axis of the inner detection system and a local geomagnetic field and local gravitational acceleration are calculated at any time t, and a direction vector of the axis of the inner detection system is obtained through the included angles; the position of the inner detection system at any time is obtained; and whether leakage exists is judged through comparison of processed sound signals, pressure signals and temperature signals, and leakage rate is estimated. The inner detection system for submarine pipelines and the detection method of the inner detection system achieve detection of little leakage, improve detection accuracy, reduce detection difficulty and cost, and shorten detection period.