The objective of this paper is to model and design a low-level turn-to-turn fault (T2TF) protection scheme for a magnetically controlled shunt reactor (MCSR), during incipient stage under 10% to 100% operating capacity. Due to the structural and functional differences of all the three windings in extra-high voltage (EHV) MCSR, a separate mechanism of detecting a T2TF in each winding is necessary. For this purpose, a detailed mathematical and structural analysis of the model is performed, and a comprehensive protection scheme based on the internal changes in magnetic and electric parameters of the windings is formulated to detect 3% T2TF in power windings (PWs), control windings (CtrWs), compensation windings (CpWs), and to differentiate it from other abnormalities. The main idea of the scheme is to perform the currents magnitude comparison of respective winding with the predefined settings values and decide necessary action. The proposed scheme is also capable of identifying the faulty winding along with faulty phase. The scheme is tested under different operating capacities (10%, 50%, 100%), and other types of unusual conditions, i.e., direct energization, pre-excited energization, power regulation, internal and external faults. The results demonstrate the effectiveness of the proposed scheme. The work of this paper is applicable in the areas of power system transmission and power system protection. The simulations are carried out on MATLAB/Simulink-based models.