A method for a protocol in digital asset trading includes step as follow. Trading information is exchanged between the first and the second nodes, in which a first digital currency belonging to the first node and a second digital currency belonging to the second node are expected to be exchanged, and prices of the first and second digital currencies are time-dependent. An atomic swap script and a smart contract are generated. A compensation fee to be paid to the second node by the first node is computed. A redeeming or refunding event is performed in response to the atomic swap script and the smart contract with paying the compensation fee to the second node, in which the compensation fee is dependent on the prices of the first and second digital currencies such that is time-dependent.