Previous studies have confirmed that the nanohydroxyapatite/polyamide-66 (n-HA/PA66) cage is an ideal alternative material for degenerative lumbar disease (DLD) comparable to the polyether ether ketone (PEEK) cage due to its similar radiographic fusion, subsidence rate, and clinical results. However, these studies were restricted to one-level surgery. The aim of this study was to analyze the long-term clinical and radiologic outcomes between n-HA PA66 cage and PEEK cage for patients with multi-level degenerative lumbar diseases (DLDs). We retrospectively reviewed all patients who underwent multi-level transforaminal lumbar interbody fusion (TLIF) from June 2010 to December 2016 with a minimum 6-year follow-up. Matched-pair analysis was performed using a 1-to-1 closest neighbor approach to match patients who received an n-HA PA66 cage with those who received a PEEK cage. Clinical outcomes and radiographic evaluations were compared between the two groups. The independent student's t-test and χ2 -test were applied to compare the differences between groups. At the end of the propensity score matching (PSM) analysis, 48 patients from n-HA/PA66 group were matched to 48 patients in the PEEK group. No significant difference was observed in cage subsidence and bony fusion except for adjacent segment degeneration (ASD). The occurrence of ASD was 14.58% (7/48) in the n-HA/PA 66 group, which was significantly less than that in the PEEK group (33.33% [16/48]) (p = 0.031). Although the intervertebral space height (IH), segmental angle (SA) and lumbar lordosis (LL) significantly increased after surgery in both groups, there was no significant difference at any time point after surgery (p > 0.05). The visual analogue scale (VAS) and Oswestry disability index (ODI) scores significantly improved in both groups at 3m postoperative, 1y postoperative and at final follow-up. However, there were no significant differences in the VAS and ODI score at any time point (p > 0.05). The total complications and re-admission rate were not different between the two groups. Overall, our data suggest that the outcomes of n-HA/PA66 cage group are comparable to those of the PEEK cage group, with a similar high fusion rate and low cage subsidence rate as PEEK cages, except its lower rate of ASD occurrence.