The invention discloses a shallow water deposit and water sample collection device and using method thereof.The device comprises a sampling tube, hole sampling tube cap, a piston pushing rod, an upper choke plug, a lower choke plug, a check valve, an extension rod, a deposit collection head, a water sample collection head and a deposit slicing head.When water is collected, the upper end of the sampling tube is sequentially connected with the hole sampling tube cap, the check valve and the extension rod, and the lower end of the sampling tube is connected with the water sample collection head; when deposit is collected, the upper end of the sampling tube is sequentially connected with the hole sampling tube cap, the check valve and the extension rod, and the lower end of the sampling tube is connected with the deposit collection head; when the deposit is stored, the upper end of the sampling tube is connected with the upper choke plug, and the lower end of the sampling tube is connected with the lower choke plug; when the deposit is cut, the upper end of the sampling tube is inserted into the piston push rod, and the lower end of the sampling tube is connected with the deposit slicing head.Deposit collection and water sample collection are integrated, in-situ layering characteristics of samples can be stored, the structure is simple, the manufacturing cost is low, carrying is easy, use is convenient, and the device is multifunctional and has the wide application value.