The subjectivity of morphological assessment and the overlapping pathological features of different subtypes of myeloproliferative neoplasms (MPNs) make accurate diagnosis challenging. To improve the pathological assessment of MPNs, we developed a diagnosis model (fusion model) based on the combination of bone marrow whole-slide images (deep learning [DL] model) and clinical parameters (clinical model). Thousand and fifty-one MPN and non-MPN patients were divided into the training, internal testing and one internal and two external validation cohorts (the combined validation cohort). In the combined validation cohort, fusion model achieved higher areas under curve (AUCs) than clinical or DL model or both for MPNs and subtype identification. Compared with haematopathologists with different experience, clinical model achieved AUC which was comparable to seniors and higher than juniors (p = 0.0208) for polycythaemia vera. The AUCs of fusion model were comparable to seniors and higher than juniors for essential thrombocytosis (p = 0.0141), prefibrotic primary myelofibrosis (p = 0.0085) and overt primary myelofibrosis (p = 0.0330) identification. In conclusion, the performances of our proposed models are equivalent to senior haematopathologists and better than juniors, providing a new perspective on the utilization of DL algorithms in MPN morphological assessment.