As the size and complexity of reliability systems improve continuously, multiple performance levels and multiple failure modes of these system structures make related modeling and analysis more difficult. Multi-state Signature theory is the key to dealing with this problem and also an important and difficult point in the research field of Signature nowadays. The present project will go deep into reliability problems of multi-state systems basing on Signature theory. First, indexes such as multi-state/multi-state joint/multi-state ordered (survival) Signature will be proposed based on characteristics of practical systems. Next, stochastic properties of these indexes will be analyzed to describe structural characteristics of multi-state reliability systems deeply. Then, transformation formulas of these indexes will be derived to provide a simple and efficient way to compare multi-state system structures of different sizes. Finally, effective general computation methods will be presented for three different situations respectively, namely multi-state systems with binary-state components, binary-state systems with multi-state components, and systems with modules. Results of this project are not only an essential supplement and improvement to Signature theory, but also of great practical significance to reliability improvements of complex systems.