Chronic pulmonary aspergillosis (CPA) has been reported to be associated with poor prognosis in non-tuberculous mycobacteria (NTM)-pulmonary disease (PD) patients. However, whether isolation of species is associated with poor outcome or mostly just the reflection of colonization is a widely debated issue and a yet unsolved question. We conducted this single-centered retrospective cohort study of 409 NTM-PD patients to assess the impacts and prevalence of isolation and CPA development. The median observation time was 85 months. species were isolated from 79 (19.3%) and 23 (5.6%) developed CPA. Isolation of species was not associated with mortality in NTM-PD patients ( = 0.9016). Multivariate logistic regression analysis revealed that higher CRP ( = 0.0213) and AFB stain positivity ( = 0.0101) were independently associated with isolation. Different mycobacterial species were not associated with isolation. Survival curves for patients with CPA diagnosis were significantly and strikingly different from those without ( = 0.0064), suggesting that CPA development severely affects clinical outcome. Multivariate logistic regression analysis revealed that the use of systemic steroids ( = 0.0189) and cavity ( = 0.0207) were independent risk factors for the progression to CPA. Considering the high mortality rate of CPA in NTM-PD, early diagnosis and treatment are essential to improve outcomes for NTM-PD patients.