Flexible magnetic continuum robots (MCRs) can be fabricated in small dimensions with great manipulability as their tips can deflect under fields, without the need for complicated mechanical structures to govern control, and it helps improve operating conditions during retrograde intrarenal surgery (RIRS). However, the limited effective workspace of an electromagnet-based magnetic navigation system (MNS) influences the practical applications. Herein, the method of steering a flexible MCR in the enlarged workspace of a common MNS for RIRS is presented. First, the field heterogeneity is parameterized to quantitatively analyze its influence on the motion of the MCR. Then, a kinematic model of the MCR is constructed, by coupling the heterogeneous-field and Cosserat-rod models, to predict its large deformation in the enlarged workspace with constraints. The model is validated with the maximum mean error of 0.53 ± 0.39 mm for the tip position in all the experiments. It is demonstrated that the effective workspace can be enlarged to 75% of the physical workspace. In addition, experiments in phantoms, which simulate two challenges during RIRS, are performed to prove its manipulability. This study enlarges the effective workspace of the MNS, which helps expand the practical application of the MCR.