Based on time-varying characters of spacecraft propulsion system and stochastic properties, the semi-qualitative fault isolation method which combines the Z-test and Analytical Redundancy Relations (ARRs) has been proposed. Firstly, based on the insight of state spatial alternation, it is achievable to mining time-invariant structural characters space using ARRs for Spacecraft Propulsion System which is built on the Diagnostic Bond Graph, and by the tendency analysis of the residuals of ARRs, the time-invariant fault signature matrix with change direction can be established. Secondly, the Z-test for robust qualitative residual generation to established observed signature against infection from multi-uncertainty is used, and then faults are isolated by comparison of observed signature and fault signature. Through the analysis of isolation results of a spacecraft propulsion system, it shows that the method is valid for overcoming the challenges from establishing time-varying diagnostic criteria and the jamming from stochasticity not only in the system model, but also in the measurements, which improves the robustness in fault isolation.