The recent novel temperature-modulated differential scanning calorimetry (DSC) (MDSCTM TA Instruments) technique has been applied to characterize the thermal properties of Ge–Se chalcogenide glasses in the glass transition region. All samples in this work were given the same thermal history by heating to a temperature above the glass transition, equilibrating, and then cooling at a rate of 5 °C/min to a temperature of 20 °C. The reversing and nonreversing heat flows through the glass transformation region during both heating and cooling schedules were measured, and the values of the parameters Tg, ΔH, Cp, and ΔCp, which characterize the thermal events in the glass transition region, were determined. The ability of determining the reversible heat flow in MDSC enables an accurate measurement of the true heat capacity (that normally associated with reversible heat flow), which could not be done hitherto in conventional thermal analysis where the detected heat flow is the total heat flow, the sum of reversing and nonreversing heat flows. The structurally controlled parameters Tg, ΔH, Cp, and ΔCp reveal extrema when the Ge–Se glass system reaches the average coordination number 〈r〉 = 2.67 at 33.3 at.% Ge which corresponds to the stoichiometric composition GeSe2. We also observed extrema in the composition dependence of the above thermal parameters at 20.0 and 40.0 at.% Ge which correspond to stoichiometric compositions GeSe4 and Ge2Se3 with average coordination numbers 2.40 and 2.80, respectively. No such clear local maxima below and above the 33.3 at.% Ge composition could be observed previously in thermal analysis. We compare our MDSC results with previously published works on glass transition in Ge–Se glasses and discuss the results in terms of recent structural models for chalcogenide glasses.