The present invention provides a reactor physical startup method and system. The method includes the following steps that: S1, geometrical modeling is performed on a reactor, so that the geometric model of the reactor is obtained; S2, the geometric information and nuclide distribution information of corresponding three-dimensional fuel components are obtained according to the geometric model; S3,the calculation model of the core of the reactor is built according to the geometric information, the nuclide distribution information and the geometric model; S4, the parameters of the reactor are obtained based on the calculation model of the core of the reactor; and S5, the reactor is started according to the parameters of the reactor. With the reactor physical startup method and system of theinvention adopted, more elaborate modeling can be realized, and therefore, the calculation accuracy and measurement accuracy of the physical startup parameters of the reactor can be improved, the modeling process of the reactor can be simplified, and a human error rate can be reduced.