At present, the influence of Modic changes (MCs) on postoperative fusion rate of lumbar interbody fusion (LIF) is mainly focused on the medium- and long-term fusion rate, while the short-term fusion rate has not been reported. The aim of this study was to compare the short-term fusion rate of lumbar degenerative disease patients with and without MCs after single level transforaminal lumbar interbody fusion (TLIF). In this retrospective and matched-pair case control study, we included 100 patients who underwent TLIF from January 2017 to January 2020 and had at least two follow-up visits over a two-year period. Fifty patients with MCs (MCs group) were matched with 50 patients without MCs (non MCs group) for age, sex, surgical level, diagnosis, operative time, and intraoperative blood loss. We collected the X-ray and computed tomography (CT) data of patients from 3 months to 2 years after the operation to assess bony fusion and the cage union ratio. According to the type of cage, the MCs group was further divided into the nano-hydroxyapatite/polyamide 66 (n-HA/PA66) group and polyetheretherketone (PEEK) group, and the fusion performance between the two groups was compared. Finally, age, sex, body mass index (BMI), smoking and cage type were included in the logistic regression model for risk factor analysis. The bony fusion rates in the MCs group at 3 months, 6 months, 1 year and 2 years after surgery were significantly lower than those in the non MCs group (P < 0.05) (23.8% vs 62.5%, 52.6% vs 78.9%, 61.1% vs 83.3%, 74.0% vs 90.0%). The average coronal cage union ratios of the upper and lower endplates in the MCs group were significantly lower than those in the non MCs group (54.3% ± 17.5% vs 75.0% ± 17.2%, P < 0.05; 73.3% ± 12.0% vs 84.9% ± 8.0%, P < 0.05). Similarly, analogous results were obtained by comparing the MCs and non MCs groups' three-dimensional CT sagittal plane images (62.5% ± 16.5% vs 76.1% ± 12.4%, P < 0.05; 67.0% ± 13.9% vs 79.8% ± 11.5%, P < 0.05). Short-term fusion rates were lower in the MCs group than in the non MCs group. The coronal and sagittal cage union ratio in the MCs group was lower than that in the non MCs group. The fusion performance of n-HA/PA66 and PEEK cages in the MCs group was comparable.