Background: There is strong evidence for the co-occurrence of mental health conditions and alcohol problems, yet physical health outcomes among this group are not well characterised. This study aimed to identify clusters of physical health conditions and their associations with mental health and problematic alcohol use in England’s general population. Methods: Cross-sectional analysis of the 2014 Adult Psychiatric Morbidity Survey (N = 7546) was conducted. The survey used standardised measures of problematic alcohol use and mental health conditions, including the Alcohol Use Disorders Identification Test (AUDIT) and the Clinical Interview Schedule-Revised. Participants self-reported any lifetime physical health conditions. Latent class analysis considered 12 common physical illnesses to identify clusters of multimorbidity. Multinomial logistic regression (adjusting for age, gender, ethnicity, education, and occupational grade) was used to explore associations between mental health, hazardous drinking (AUDIT 8 +), and co-occurring physical illnesses. Results: Five clusters were identified with statistically distinct and clinically meaningful disease patterns: ‘Physically Healthy’ (76.62%), ‘Emerging Multimorbidity’ (3.12%), ‘Hypertension & Arthritis’ (14.28%), ‘Digestive & Bowel Problems’’ (3.17%), and ‘Complex Multimorbidity’ (2.8%). Having a mental health problem was associated with increased odds of ‘Digestive & Bowel Problems’ (adjusted multinomial odds ratio (AMOR) = 1.58; 95% CI [1.15–2.17]) and ‘Complex Multimorbidity’ (AMOR = 2.02; 95% CI [1.49–2.74]). Individuals with co-occurring mental health conditions and problematic alcohol use also had higher odds of ‘Digestive & Bowel Problems’ (AMOR = 2.64; 95% CI [1.68–4.15]) and ‘Complex Multimorbidity’ (AMOR = 2.62; 95% CI [1.61–4.23]). Conclusions: Individuals with a mental health condition concurrent with problematic alcohol use experience a greater burden of physical illnesses, highlighting the need for timely treatment which is likely to include better integration of alcohol and mental health services.