Upper limb (UL) motor function recovery, especially distal function, is one of the main goals of stroke rehabilitation as this function is important to perform activities of daily living (ADL). The efficacy of the motor-imagery brain-computer interface (MI-BCI) has been demonstrated in patients with stroke. Most patients with stroke receive comprehensive rehabilitation, including MI-BCI and routine training. However, most aspects of MI-BCI training for patients with subacute stroke are based on routine training. Risk factors for inadequate distal UL functional recovery in these patients remain unclear; therefore, it is more realistic to explore the prognostic factors of this comprehensive treatment based on clinical practice. The present study aims to investigate the independent risk factors that might lead to inadequate distal UL functional recovery in patients with stroke after comprehensive rehabilitation including MI-BCI (CRIMI-BCI). This prospective study recruited 82 patients with stroke who underwent CRIMI-BCI. Motor-imagery brain-computer interface training was performed for 60 min per day, 5 days per week for 4 weeks. The primary outcome was improvement of the wrist and hand dimensionality of Fugl-Meyer Assessment (δFMA-WH). According to the improvement score, the patients were classified into the efficient group (EG, δFMA-WH > 2) and the inefficient group (IG, δFMA-WH ≤ 2). Binary logistic regression was used to analyze clinical and demographic data, including aphasia, spasticity of the affected hand [assessed by Modified Ashworth Scale (MAS-H)], initial UL function, age, gender, time since stroke (TSS), lesion hemisphere, and lesion location. Seventy-three patients completed the study. After training, all patients showed significant improvement in FMA-UL (Z = 7.381, = 0.000), FMA-SE (Z = 7.336, = 0.000), and FMA-WH (Z = 6.568, = 0.000). There were 35 patients (47.9%) in the IG group and 38 patients (52.1%) in the EG group. Multivariate analysis revealed that presence of aphasia [odds ratio (OR) 4.617, 95% confidence interval (CI) 1.435-14.860; < 0.05], initial FMA-UL score ≤ 30 (OR 5.158, 95% CI 1.150-23.132; < 0.05), and MAS-H ≥ level I+ (OR 3.810, 95% CI 1.231-11.790; < 0.05) were the risk factors for inadequate distal UL functional recovery in patients with stroke after CRIMI-BCI. We concluded that CRIMI-BCI improved UL function in stroke patients with varying effectiveness. Inferior initial UL function, significant hand spasticity, and presence of aphasia were identified as independent risk factors for inadequate distal UL functional recovery in stroke patients after CRIMI-BCI.