Aim To explore the characteristics of heart rate variability (HRV) and its short-term prognosis in patients with chronic heart failure complicated with type 2 diabetes mellitus (T2DM). Methods 105 patients with chronic heart failure were selected as heart failure group. Patients were divided into simple heart failure group and heart failure with T2DM group. 40 patients with organic heart disease without heart failure who were hospitalized at the same time were selected as control group. To collect the general data, the results of echocardiography and 24-hour ambulatory electrocardiogram of patients in each group, including the standard deviation of the mean of sinus rhythm normal-to-normal intervals (SDNN), ratio of the total number of sinus R-R intervals to the height of the histogram of sinus R-R intervals (TRI), the square root of the mean of the sum of the squares of differences between adjacent NN intervals (rMSSD) and the proportion of differences between successive R-R intervals that are greater than 50 ms (PNN50). The differences of clinical data between control group and heart failure group, heart failure subgroups were compared. The HRV indexes of different diabetic course in heart failure with T2DM group were analyzed. The patients in heart failure group were followed up for 3 months to compare the number of re-hospitalization due to heart failure. Results The course of disease, the total cost, B-type natriuretic peptide (BNP), left ventricular end diastolic diameter (LVEDd), the slowest heart rate and the average heart rate were higher in the heart failure group than those in the control group, and the hemoglobin (Hb), left ventricular ejection fraction (LVEF), cardiac output (CO), SDNN, TRI, rMSSD and PNN50 were lower than those in the control group. The multivariate logisitic regression analysis showed that the course of disease, BNP and the slowest heart rate were independent risk factors for heart failure in patients with organic heart disease. Total cost, the number of β-blocker used, course of disease, fasting blood glucose, BNP, NYHA class Ⅳ cases, the average heart rate and the fastest heart rate were higher in heart failure with T2DM group than those in simple heart failure group, and SDNN, TRI, rMSSD and PNN50 were lower than those of simple heart failure group (P<0.05). Fasting blood glucose was associated with T2DM in patients with heart failure. In patients with T2DM more than 10 years, the levels of rMSSD and PNN50 decreased significantly (P<0.05). The number of re-hospitalization in heart failure complicated with T2DM group was higher than that in simple heart failure group (P<0.05). Conclusions The heart autonomic nervous function in patients with chronic heart failure is lower than in patients with organic heart disease without heart failure. T2DM mellitus can further decrease the HRV of patients with chronic heart failure, damage the heart autonomic nervous function and affect the short term prognosis of patients with chronic heart failure.