The invention discloses a method for utilizing a simulation molecular dynamics method to determine afterloading source residence time. The method is used for solving the problem in the prior art that the residence positions are large in number and the dosage reference points cannot correspond to the residence positions in a one-to-one correspondence mode due to complex clinical conditions. The method includes the following steps: 1 adopting the following expression to calculate the dosage of each residence position at the position of the corresponding dosage control point according to the position relation between the residence positions and the dosage control points; 2 forming an evaluation function according to the difference between calculation dosage and prescription dosage at the dosage control points and the time difference between the adjacent residence points; 3 acquire a partial derivative through the time tk according to the above expression to obtain the expression (3); 4 approximating the above expression into a molecular dynamic equation to obtain mutual action force between molecules; 5 adopting the following expression to conduct iteration and acquiring different residence time by changing the tvalue continuously in the iteration process.