Few studies have investigated the characteristics of stroke inpatients after post-acute care (PAC) rehabilitation, and few studies have applied propensity score matching (PSM) in a natural experimental design to examine the longitudinal impacts of a medical referral system on functional status. This study coupled a natural experimental design with PSM to assess the impact of a medical referral system in stroke patients and to examine the longitudinal effects of the system on functional status. The intervention was a hospital-based, function oriented, 12-week to 1-year rehabilitative PAC intervention for patients with cerebrovascular diseases. The average duration of PAC in the intra-hospital transfer group (31.52 days) was significantly shorter than that in the inter-hospital transfer group (37.1 days) (p < 0.001). The intra-hospital transfer group also had better functional outcomes. The training effect was larger in patients with moderate disability (Modified Rankin Scale, MRS = 3) and moderately severe disability (MRS = 4) compared to patients with slight disability (MRS = 2). Intensive post-stroke rehabilitative care delivered by per-diem payment is effective in terms of improving functional status. To construct a vertically integrated medical system, strengthening the qualified local hospitals with PAC wards, accelerating the inter-hospital transfer, and offering sufficient intensive rehabilitative PAC days are the most essential requirements.