Purpose To determine and compare the performance of zero echo imaging (ZTE) with conventional MRI sequences on lumbar osseous morphology in patients suspected with lumbar degeneration with multi-slice computed tomography (MSCT) as standard reference. Methods 22 subjects with concerned lumbar degeneration were recruited. All subjects were scanned with ZTE sequence after routine conventional MR sequences on a 3.0 T system and also received MSCT examination. Image quality was assessed. The quantitative and qualitative parameters of lumbar osseous morphology on MSCT, ZTE and MRI images were evaluated by three musculoskeletal radiologists independently. Inter-reader and inter-modality reliability and the difference between the modalities were calculated. Results There was no difference for the osseous parameters between modalities, including axial orientation (p = 0.444), IAD (p = 0.381), lateral recess (p = 0.370), pedicle width (p = 0.067), pedicle height (p = 0.056), and osteophyte grade (p = 0.052). The measurement of the foramina diameter was statistically different between conventional MRI and MSCT (p < 0.05) but not between the MSCT and ZTE (p = 0.660). Conventional MRI was more likely to miss cortical bone abnormalities. ZTE appeared blurrier in cortical bone than MSCT, especially in cases with severe lumbar degeneration. The inter-reader agreement between MSCT and ZTE-MRI was higher than between MSCT and conventional MRI. Conclusions ZTE-MRI could offer more cortical bone details than conventional MRI images and might be a valid alternative to CT for lumbar osseous morphology assessment to some extent.