As large language models (LLMs) become increasingly integrated into applications serving users across diverse cultures, communities and demographics, it is critical to align LLMs with pluralistic human values beyond average principles (e.g., HHH). In psychological and social value theories such as Schwartz's Value Theory, pluralistic values are represented by multiple value dimensions paired with various priorities. However, existing methods encounter two challenges when aligning with such fine-grained value objectives: 1) they often treat multiple values as independent and equally important, ignoring their interdependence and relative priorities (value complexity); 2) they struggle to precisely control nuanced value priorities, especially those underrepresented ones (value steerability). To handle these challenges, we propose COUPLE, a COUnterfactual reasoning framework for PLuralistic valuE alignment. It introduces a structural causal model (SCM) to feature complex interdependency and prioritization among features, as well as the causal relationship between high-level value dimensions and behaviors. Moreover, it applies counterfactual reasoning to generate outputs aligned with any desired value objectives. Benefitting from explicit causal modeling, COUPLE also provides better interpretability. We evaluate COUPLE on two datasets with different value systems and demonstrate that COUPLE advances other baselines across diverse types of value objectives.