Variation equivalence concerns the mechanism by which multiple types of error sources (e.g., the fixture error, machine tool error and datum error) result in identical variation patterns on part features. This phenomenon poses challenges in distinguishing the effects from multiple variation sources and thereby diagnoses the root cause. This paper improves the root cause diagnosis taking into account the variation equivalence phenomenon. Variation equivalence model is established to study the equivalent properties among different variation sources. Through exploring a number of possible equivalent variations scenarios, an equivalent variation patterns library is created for an improved interpretation of fault patterns by considering variation equivalence among multiple error sources. Combined with the library, this paper proposes an excitation-response path method to distinguish multiple error sources under variation equivalence. A case study verifies the diagnostic approach