Clear aligner therapy (CAT) is increasingly used in orthodontic practice. However, the biomechanical effectiveness and predictability of tooth movement in complex cases should be further clarified and enhanced. This article provides a systematic review of the biomechanical mechanisms underlying four common complex treatment modalities in CAT, namely, molar distalization, arch expansion, vertical tooth movement, and extraction cases, and summarizes current clinical strategies, such as overcorrection design, attachment, mini-screw-assisted anchorage, and intra-/inter-arch elastic traction. The role of these strategies in improving tooth movement control and treatment efficacy is elucidated, and potential future developments is discussed. The findings can offer a theoretical basis and practical guidance for optimizing CAT and improving the control ability and predictability of treatment outcomes.