Computer aided design (CAD) models reflect design goals, intentions, and functions so that they are the key intellectual properties of companies. In a Cloud manufacturing environment, how to effectively protect the sensitive feature information for a model owner while enabling the owner to flexibly share the rest of the CAD model with collaborators is an important yet challenging research issue. In this paper, an innovative partial encryption approach, which is able to represent a CAD model into the granularity of sharing information in order to address various collaboration scenarios and customized requirements from the model owner and collaborators, is presented. The approach is composed of a customized encryption algorithm for a CAD model, a key based customized authorization algorithm for collaborators to decrypt shared features in the model, and a customized geometric transformation method to support the effective protection model-based visualization of the model for collaboration. With this approach, a CAD model can be flexibly encrypted to realize partial sharing of features and safe protection of the rest of the model according to collaboration requirements. Meanwhile, during encryption and decryption, the CAD model is always manifold no matter which feature is encrypted or decrypted to ensure user friendliness, model validity, and robustness of the approach. A case study is used to verify and illustrate the effectiveness of the approach. This research is a new attempt to design a content-based and customized encryption approach applicable to CAD model-based collaboration in a Cloud manufacturing environment.