Nano-hydroxyapatite and its composites(nHA) have been widely used as grafts in inter-vertebral fusion. However, the safety and efficacy of the graft in inter-vertebral fusion is controversial. This meta-analysis aimed at evaluating the safety and efficacy of nHA and non-hydroxyapatite grafts (noHA) (autologous bone, etc.) in inter-body fusion. A comprehensive search was performed in electronic database as follows: PubMed, EMBASE, the Cochrane Library, Web of Science, and China National Knowledge Internet (CNKI) from inception until October 2022. Clinical studies on the effect of nHA and noHA in spinal fusion were collected. Analysis of outcome indicators using RevMan 5.4 statistical software. The meta-analysis showed that the operation time of patients who underwent inter-body fusion with nHA grafts was less than that of patients who underwent noHA (p < 0.05). Compared with the noHA group, the nHA group can achieve similar clinical effects in the fusion rate(OR = 1.29,95%CI: 0.88 to 1.88,p = 0.19),Subsidence rate(OR = 1.2,95%CI:0.44 to 3.28,p = 0.72), inter-vertebral space height(SMD = 0.04,95%CI:-0.08 to 0.15,p = 0.54),Cobb angle(SMD = 0.21,95%CI: 0.18 to 0.6,p = 0.21),Blood loss(SMD = -36.58,95%CI: -81.45 to 8.29,p = 0.11),operative time in 12 months(SMD = -5.82,95%CI: -9.98 to -1.67,p = 0.006) and in the final follow-up(SMD = -0.38,95%CI: -0.51 to -0.26,p < 0.00001),ODI(SMD = 0.68,95%CI: -0.84 to 2.19,p = 0.38), VAS(SMD = 0.17,95%CI: -0.13 to 0.48,p = 0.27) and adverse events(OR = 0.98,95%CI: 0.66 to 1.45,p = 0.92), and the differences are not statistically significant. This meta-analysis suggests that nHA matrix grafts are similar to noHA grafts in the safety and efficacy of spinal reconstruction, and are an ideal material for inter-vertebral bone grafting.