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Background: This study aimed to assess the reliability, validity, and factor structure of the Patient Health Questionnaire-9 (PHQ-9) and its two subscales (PHQ-2, PHQ-1) for screening major depression disorder (MDD) in primary care elderly patients in Taiwan. Method: A total of 634 participants aged ≥60 years were enrolled from the primary care settings. They completed PHQ-9, and Short Form of Quality of Life Enjoyment and Satisfaction Questionnaire (Q-LES-Q-SF). After that, they were interviewed by using Schedule for Clinical Assessments in Neuropsychiatry (SCAN) and 17-item of Hamilton Rating Scale (HAMD-17). Result: The PHQ-9 demonstrated acceptable internal consistency (α = 0.77), test-retest reliability (intraclass correlation coefficient = 0.79), and concurrent validity with HAMD-17 (r = 0.66; p < 0.001). Exploratory factor analysis yielded 2-factor structure consisted of non-somatic (13.3% variance) and somatic (38.8% variance) dimensions. The correlations between PHQ-9 with Q-LES-Q-SF (whole and two subscales) were moderate (r range −0.47 to −0.53, all ps < 0.001). Using SCAN as gold standard, the optimal cutoff score of ≥6 for PHQ-9 demonstrated good sensitivity and specificity for detecting MDD (1.00 and 0.85, respectively). The screening accuracy of the two items version was also acceptable (PHQ-2 score ≥ 2: sensitivity 0.93; specificity 0.90; PHQ-1 score ≥ 1: sensitivity 1.00; specificity 0.77). Conclusion: The Chinese versions of the PHQ-9 and its two subscales (PHQ-2 and PHQ-1) are valid and reliable to screen MDD in primary care elderly patients in Taiwan and could be proper alternatives to Geriatric Depression Scale 15-item version.