Animation is widely acknowledged for its dynamic visualization of information and plays an ever-greater role in education. However, this growth has not been accompanied by well-informed studies that focus on the semiotic mode of animation (e.g. Berney & Bétrancourt, 2016). This thesis proposes a systematic model of animation by drawing on stratification and metafunction, two important concepts for describing semiotic resources in the tradition of Social Semiotics and Systemic Functional Semiotics. Animation is modelled as a semiotic mode consisting of an expression plane and a content plane. Systems are proposed on the expression plane to describe elements (changing visuals) in a shot as well as the LAYOUT and VISUAL RHYTHM of elements in a shot. This thesis explores the ideational and textual meaning of animation on its content plane. Ideational meaning is concerned with the way animation construes human experience (entities, figures and figure complexes). The ways ideational meaning units are adjusted in PROMINENCE are explored as choices in a textual system. This thesis also explores intermodal relations between animation and language in online science animated videos. A framework is proposed to explain the synergy between animation and language in terms of stratificational integration and instantial complementarity. This thesis contributes to semiotic studies and science education research in three ways. First, it introduces the first systematic description of animation based on a corpus of online science animations. Second, it offers a theoretical model of intermodal relations which has the potential to be applied to multimodal discourse analysis involving different combinations of semiotic modes. Third, it facilitates an understanding of science knowledge organized by different semiotic modes.