In recent years, several comparative life cycle analyses have shown that increasing the use of wood in buildings can reduce the life cycle primary energy use and carbon emission of buildings. This study reviews the life cycle inventory methodology of primary energy use and carbon emissions, based on ecoinvent database, considering different modelling choices for (i) materials heating values; (ii) biogenic carbon; (iii) calcination and carbonation processes; (iv) electricity production scenarios; (v) impact distribution of multi-functional processes; (vi) post-use benefits. The analysis relates to the standards while the implication of different modelling choice is shown by comparing the primary energy use and carbon emission in the production and end-of-life stages of a multi-storey residential building with concrete, cross laminated timber and modular timber structures, respectively. The results highlight the displacement between different modelling choices in terms of primary energy use and carbon emissions. Such modelling options especially influence the LCA results in the product stage and beyond the end of life stage, and especially wood- and/or cement-based materials.