Item response theory (IRT) is a modern psychometric framework for estimating respondents’ latent traits (e.g., ability, attitude, and personality) based on their responses to a set of questions in psychological tests. The current study adopted an item response tree (IRTree) method, which combines the tree model with IRT models for handling the sequential process of responding to a test item, to score individual moral inclination for the CNI test—a broadly adopted model for examining humans’ moral decision-making with three parameters generated: sensitivity to moral norms, sensitivity to consequences, and inaction preference. Compared to previous models for the CNI test, the resulting EIRTree-CNI Model is able to generate individual scores without increasing the number of items (thus, less subject fatigue or compromised response quality) or employing a post hoc approach that is deemed statistically suboptimal. The model fits the data well, and the subsequent test also supported the concurrent validity and the predictive validity of the model. Limitations are discussed further.