A transfer and online detection system for deep-sea sediment samples and an application method thereof are provided. A sample gripping and feeding device, a sample segment cutting device, a sample online detection device, a high-pressure ball valve and a pressure-retaining drill disengaging device of the system are coaxially connected with one another. A seawater booster pump is connected with a water inlet ball valve, and a valve control panel is connected with the sample gripping and feeding device, the sample segment cutting device, the high-pressure ball valve and the pressure-retaining drill disengaging device. The pressure-retaining drill disengaging device is configured for disengaging an inner barrel and an inner barrel joint, and the sample gripping and feeding device and the sample segment cutting device are configured for gripping and cutting core samples, and conveying the cut core samples into a subsample pressure-retaining storage cylinder for storage.