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By choosing appropriate candidate reference genes (CRGs) and standardizing qPCR data, more accurate experimental data can be obtained. Herein, the expression stability of alpha-tubulin1 (TUA1), beta-tubulin (TUB), beta-tubulin 1 (TUB1), beta-tubulin 5 (TUB5), actin 1 (ACT1), actin 97 (ACT97), molecular chaperone dnaj (DNAJ), adenine phosphoribosyl transferase (APT), and histone H4 (HIS4) genes from Paulownia fortunei (Seem.) Hemsl. under different experimental conditions (different tissues, drought, salinity, Cd, and Cr treatments) was assessed with four statistical tools: RefFinder, BestKeeper, NormFinder, and geNorm. Notably, TUA1 and TUB5 were identified as CRGs for different tissues, ACT97 and TUB1 for drought treatment, ACT97 and APT for salinity treatment, TUB1 and ACT97 for Cd treatment, and DNAJ, TUB1 and TUB5 for Cr treatment. Furthermore, the results of "total" group, V4/V5 > 0.15 and V5/V6 < 0.15 revealed that the CRGs or gene combinations, which could meet all the test conditions, were not easy to identify. To further verify the reliability of CRGs, the expression levels of paulownia fortunei cellulose synthase A catalytic subunit2 (PfCesA2) and paulownia fortunei glutathione reductase (GR) genes were analysed. The expression patterns were different when the unstable CRGs were used for normalization compared to when the stable CRGs and combination were used for normalization. This study will lay a foundation for study on the expression levels of key genes from P. fortunei seedlings.