Background As the global aging process accelerates, the older population is increasing annually, with the majority suffering from one or more chronic diseases. Due to the influence of chronic disease comorbidity, frailty among the older is widespread. Therefore, early identification of frailty in older adults with comorbidities from a comprehensive perspective, along with proactive measures for prevention and timely intervention, becomes an inevitable requirement for healthy aging. This study aimed to identify the entry point of frailty management in the older with multimorbidity in the community and clarify the focus of frailty management. Methods A national cross-sectional survey of 1056 older adults with comorbidities in 148 cities across China was conducted. Frailty was assessed using the Fatigue, Resistance, Ambulation, Illnesses, and Loss of weight (FRAIL) scale. Based on the health ecological model, the factors which may influence frailty were collected from five levels. Univariate and multivariate analysis were utilized to determine the factors influencing frailty. The STROBE checklist was used preparing the manuscript. Results A total of 417 patients (39.5%) reported having frailty, while 613 patients (58.0%) were in the pre-frail state. Multivariate logistic regression analysis indicate that compared with robust patients, number of comorbidities, self-efficacy, sleep quality and perceived social support are associated with frailty in older patients with comorbidities (P < 0.05). Compared to pre-frail group, factors such as number of comorbidities, gender (female), cognitive status of diseases, anxiety, having four or more comorbidities, smoking, eating habits, taking three or more different types of medication and perceived social support are associated with frailty (P < 0.05). Conclusions The prevalence of frailty among older adults with comorbidities is exceptionally high, influenced by various dimensions from health ecology perspective. Psychological care and daily behavior management should be strengthened for the frail older with multimorbidity. Precise and individualized care interventions need to be developed to help promote healthy aging.