We develop an optimization approach to model the magnetic field configuration of magnetic clouds, based on a linear force‐free formulation in three dimensions. Such a solution, dubbed the Freidberg solution, is kin to the axisymmetric Lundquist solution, but with more general “helical symmetry.” The merit of our approach is demonstrated via its application to two case studies of in situ measured magnetic clouds. Both yield results of reduced χ2 ≈ 1. Case 1 shows a winding flux rope configuration with one major polarity. Case 2 exhibits a double‐helix configuration with two flux bundles winding around each other and rooted on regions of mixed polarities. This study demonstrates the three‐dimensional complexity of the magnetic cloud structures. Plain Language Summary Magnetic clouds (MCs) are a type of magnetic field structures observed in space. They possess some well‐defined properties and have been well studied in the space age. The existing model for such a structure is a straight cylinder with no variation along its axis. They may impact Earth carrying significant amount of electromagnetic energy. They come in relatively large sizes. When encompassing the near‐Earth space environment, their impact can last for days. MCs originate from the Sun, directly born with the so‐called coronal mass ejections (CMEs) which can be seen as an ejection of large amount of solar material from telescopes aiming at the Sun. The CMEs are often accompanied by solar flares, the most energetic and explosive events in our solar system. When these happen, they release a wide range of radiations and disturbances that may adversely impact Earth with MCs being one major type of such disturbances. Therefore, studying the internal configuration of MCs is of importance to understanding their origin and impact. This study presents a more complex three‐dimensional MC model to better fit the in situ spacecraft measurements of such structures, which goes beyond the current model. Key Points First rigorous applications of a three‐dimensional (3D) model are carried out for in situ measurements of magnetic clouds (MCs) Results via the optimal fitting approach yield reduced Chi2 values close to 1 Complexity of MC flux ropes is revealed by the model showing 3D winding magnetic flux bundles