This study focused on the start-up and operating characteristics of the endogenous partial denitrification (EPD) process with different carbon sources. Two sequencing batch reactors (SBRs) with sodium acetate (SBR1#) and glucose (SBR2#) as carbon sources were operated under anaerobic/oxic (A/O) and anaerobic/anoxic/oxic (A/A/O) modes successively for 240 d. The results showed that COD removal efficiency reached 85% and effluent COD concentrations were below 35 mg/L in both SBRs. The difference was that faster absorption and transformation of sodium acetate was achieved compared to glucose (COD removal rate (CRR) was 7.54 > 2.22 mgCOD/(L·min) in SBR1# compared to SBR2#). EPD could be started up with sodium acetate and glucose as carbon sources, respectively, and desirable high nitrite accumulations were both obtained at influent NO3−−N (NO3−-Ninf) increased from 20 to 40 mg/L with nitrate-to-nitrite transformation ratio (NTR) and specific NO3−-N deduction rate (rNa) of 88.4~90% and 2.41~2.38 mgN/(gVSS·h), respectively. However, at NO3−-N of 50~60 mg/L, both the NTR and rNa in SBR1# were higher compared to SBR2# (86.5% > 83.9% and 1.58 > 1.20 mgN/(gVSS·h), respectively). Hereafter, when NO3−-N was increased by 70~90 mg/L, lower NTR and rNa were observed in SBR1# than in SBR2# (72% and 78%, 1.16 and 1.32 mgN/(gVSS·h), respectively). Additionally, similar internal carbon transformations were observed to drive EPD for NO2−−N accumulation, especially for higher and faster carbon transformation with sodium acetate as carbon source compared to glucose. However, precise control of anoxic time as the peak point of nitrite (TNi,max) was still the key to achieve high NO2−−N accumulation.