Introduction: Many Americans are not using the contraceptive method they prefer, but there has been limited study of how this may be related to health system barriers. We evaluated how such barriers to contraceptive care are related to unmet contraceptive preference in Mississippi and which contraceptive methods are preferred by those who report an unmet preference. Materials and Methods: Between September 2020 and February 2021, we used social media advertisements to recruit Mississippi residents 18–45 years of age, who were assigned female at birth, for an online survey. We asked respondents if they wanted to use a different contraceptive method or start using one, and if so, which method they preferred. We assessed barriers in the reproductive healthcare services environment (e.g., long wait for appointments, unaffordability or lack of insurance acceptance). We used multivariable-adjusted Poisson regression models to test the relationship between experiencing one or more barriers to reproductive healthcare and having an unmet contraceptive preference. Results: Among 462 eligible respondents, 37% had an unmet contraceptive preference. Most respondents (83%) reported one or more barriers to accessing office-based reproductive healthcare. Respondents who experienced a barrier had almost twice the prevalence of unmet preference as people who experienced no barrier (prevalence ratio 1.81, 95% confidence interval: 1.14–2.86). Among respondents with unmet preference, short-acting hormonal, long-acting reversible, and permanent methods were most desired. Conclusion: We find that nearly two-fifths of reproductive-aged Mississippians with capacity for pregnancy are not using their preferred contraceptive method. Structural barriers to care are very common and are significantly associated with experiencing unmet contraceptive preference, undermining reproductive autonomy.