Objective To determine the serum concentrations of N-terminal pro-type (or brain) natriuretic peptide (NT-proBNP), high sensitivity C-reactive protein (hs-CRP) and cystatin C (Cys-C) in the patients with reduced ejection fraction heart failure (HF-REF) or with preserved ejection fraction heart failure (HF-PEF) and investigate their relationship for clinical value. Methods A total of 106 outpatients with established diagnosis of heart failure (HF) in our department from November 2012 to May 2013 were prospectively subjected in this study. There were 58 cases of HF-REF (group A) and 48 cases of HF-PEF (group B). Blood samples were collected at their admission to determine the serum levels of NT-proBNP, Cys-C and hs-CRP, renal function, liver function, blood lipid, left ventricular ejection fraction (LVEF), etc. A cross-sectional study was performed in the above serum concentrations of NT-proBNP, hs-CRP and Cys-C between these 2 groups, and a correlation analysis was carried out on their heart failure indices. Results The serum levels of NT-proBNP and Cys-C were significanctly higher in the patients with HF-REF than in those with HF-PEF (both P＜0.05), but no significant difference was seen in the level of hs-CRP (P＞0.05). In patients with HF-REF, NT-proBNP was correlated with hs-CRP (r＝0.482，P＝0.009) and Cys-C (r＝0.450, P＝0.014), while hs-CRP was not correlated with Cys-C (r＝0.338, P＝0.079). In patients with HF-PEF, NT-pro BNP was only correlated significantly with Cys-C (r＝0.429, P＝0.041), but not with hs-CRP (r＝0.411, P＝0.051), while hs-CRP was correlated with Cys-C (r＝0.834, P＝0.000). Conclusion The serum concentrations of HF biomarker are different between HF-PEF and HF-REF patients. NT-pro BNP may be less useful in HF-PEF than in HF-REF.