Objective: To investigate the characteristics of functional muscle and muscle size in patients with basilar invagination (BI) and explore the effects of atlantoaxial dislocation.Methods: Eighty BI patients (BI group) and 80 age- and sex-matched asymptomatic people (control group) were included. Axial T2 magnetic resonance imaging image was used to measure the cross-sectional area (CSA) and functional CSA (FCSA). The sternocleidomastoid (SCM), longus capitis and longus colli (LCap & LC), trapezius (Trap), splenius capitis (SpCap), splenius cervicis (SpC), semispinalis capitis (SSCap), semispinalis cervicis (SSC), multifidus (MS), levator scapulae (LS) and posterior deep layer muscles (PDLM) were evaluated. Correlations between age, atlantodental interval (ADI), Chamberlain distance and muscles were observed.Results: BI group (39.4 ± 18.4 years; 33 males/47 females) exhibited significantly lower FCSA/CSA ratios than the control group in all extensor and flexor muscles, and presented smaller CSAs on the right and left Trap, SSC, LS, SCM, and left LCap & LC. FCSA/CSA ratios were significantly lower in BI patients with dislocation on the right Trap, SpCap, SpC, SSCap, MS, LS, LCap & LC, and PDLM, and the left SSCap, MS, and LCap & LC than in patients without deformity. Additionally, functional muscles of all parameters decreased with age in BI patients. Excluding children, the Trap, SpC, MS, and LS muscle sizes of BI patients tended to increase with age. ADI and Chamberlain distance tended to correlate negatively with FCSA/CSA ratio.Conclusion: The BI patients, especially those with atlantoaxial dislocation, had less functional muscles compared with the control group. Moreover, their functional muscles decreased with age more obviously.