Little is known about the oral disease burden in refugee children and associated risk factors. This cross-sectional study aimed to explore the oral hygiene status and prevalence of caries, and to investigate their association with malocclusion characteristics in a child refugee population. 606 Syrian refugee children and adolescents aged 7-19 years, registered as refugees in Jordan and residing in Zaatari camp, were recruited to the study. Oral hygiene and caries status were recorded using DMFT (mean of decayed, missing, and filled permanent teeth) and OHI-S (Simplified Oral Hygiene Index) according to WHO criteria. Oral health results were then cross tabulated with previously reported malocclusion traits for the same study sample (crowding, spacing, contact point deflection and IOTN) to detect any associations. Statistical analysis was conducted using chi-square test, independent sample t-test, one-way ANOVA, Welch test and Post Hoc testing (Gabriel and Games-Howell). Overall DMFT and OHI-S were 4.32 and 1.33 respectively with no difference between males and females. Around 40% of the sample showed ≥ 5 DMFT score. 96.1% of the sample either do not brush or brush occasionally: females showed better oral hygiene practices (P = 0.002). No significant differences in DMFT scores were noted for gender or age, other than the 7-9.9 year old group having significantly higher mean DMFT scores than all other age groups (P < 0.01);the mean of OHI-S was not significantly different between different age groups (P = 0.927). Subjects with malocclusion, specifically crowding, contact point deflection and IOTN grades 3, 4 and 5 had higher scores in both arches for OHI-S and DMFT than subjects without malocclusion traits, although this was not statistically significant for DMFT scores. Overall, patients with generalized spacing had a significantly lower OHI-S score than those without spacing (P = 0.021). Significant correlations were found between parameters of intra-arch and inter-arch relationships and oral health indices (DMFT and OHI-S). Malocclusion may increase the risk of caries and periodontal disease; the magnitude of this risk is amplified in populations with poor oral health and limited access to oral healthcare services, highlighting the need for preventive and curative oral health programs.