Energy-efficient metro operation has received increasing attention because of the energy cost and environmental concerns. This paper developed an integrated optimization model on train control and timetable to minimize the net energy consumption. The extents of train motoring and braking as well as timetable configurations such as train headway and interstation runtime are optimized to minimize the net energy consumption with consideration of utilizing regenerative energy. An improved model on train control is proposed to reduce traction energy by allowing coasting on downhill slopes as much as possible. Variations of train mass due to the change of onboard passengers are taken into account. The brute force algorithm is applied to attain energy-efficient speed profiles and an NS-GSA algorithm is designed to attain the optimal extents of motoring/braking and timetable configurations. Case studies on Beijing Metro Line 5 illustrate that the improved train control approach can save traction energy consumption by 20% in the sections with steep downhill slopes, in comparison with the commonly adopted train control sequence in timetable optimization. Moreover, the integrated model is able to significantly prolong the overlapping time between motoring and braking trains, and the net energy consumption is accordingly reduced by 4.97%.