The in-cylinder temperature information is critical for auto-ignition combustion control in diesel engines, but difficult to be directly accessed at low cost in production engines. Through investigating the thermodynamics of Tivc, cycle-by-cycle models are proposed in this paper for the estimation of in-cylinder temperature at the crank angle of intake valve closing (IVC), referred to as Tivc. An extended Kalman filter (EKF) based method was devised by utilizing the measurable temperature information from the intake and exhaust manifolds. Due to the fact that measured temperature signals by typical thermocouples have slow responses which can be modeled as first-order lags with varying time-constants, temperature signals need to be reconstructed in transient conditions. In the proposed EKF estimation method, this issue can be effectively addressed by analyzing the measurement errors and properly selecting the noises covariance matrices. The proposed estimation method was validated through a high-fidelity GT-power engine model.