In order to solve the problems for embryonics array that online fault detection is difficult to be designed, detection rate is low, and detection rate is difficult to be accurately calculated, an online fault detection method based on dual modular redundancy and a fault detection rate analysis method based on equivalence checking are proposed. A novel checker which is suitable for look up table style function module of embryonics cell is designed, and the automated design program is developed. For single stuck at fault, the circuit is first converted to an equivalence checking circuit, and then through fault injection and equivalence checking, fault detection rate can be accurately calculated. In simulations, 16 different sizes of benchmark circuits are chosen, and mapped into embryonics array. Area, delay and fault detection rate of the dual modular redundancy circuit are analyzed. Simulation results are presented with detailed area consumption data, circuit delay data and fault detection rate data, and verify that the proposed method has a high fault detection rate.