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The accumulation of single nucleotide polymorphisms (SNPs) in the displacement loop (D-loop) of mitochondrial DNA (mtDNA) has been described in many cancers. In our previous studies, we have identified cancer risk and outcome associated SNPs in the D-loop of malignant fibrous histiocytoma (MFH). In the present study, we investigated the SNPs in the D-loop of mitochondria DNA (mtDNA) for their association with age-at-onset, metastasis, and relapse using a population-based series of MFH patients. Our data showed that the SNP site of nucleotide 16304 T/C was associated with age-at-onset using the Kaplan–Meier method and compared by the log-rank test. Meanwhile, allele 152C genotype was identified to be significantly associated with a high metastasis rate in MFH patients. In addition, patients with allele 16266C were proven to have a higher relapse rate compared with 16266T at a statistically significant level. Finally, we performed a multivariate analysis with the Cox proportional hazards model. The age-at-onset of patients with the minor allele C genotype was significantly earlier than that of patients with the T genotype at the 16304 site. In summary, the analysis of genetic polymorphisms in the D-loop may help to identify patient subgroups at a high risk of early onset, high metastasis and relapse rate in MFH, thereby helping to refine therapeutic decisions.