A method and a system for detecting cross correlation in a satellite navigation receiver (SNR) in real time are provided. The SNR parallelly receives navigation signals from multiple satellites via multiple input channels. The SNR extracts ephemeris data from sub-frames of navigation data of each of the navigation signals. The SNR compares the ephemeris data of each navigation signal with the ephemeris data of another navigation signal. The SNR detects cross correlation between the navigation signals when the ephemeris data comparison results in a match and discards the navigation signal with low signal strength. The SNR also retrieves a ranging code from the sub-frames of navigation data of each navigation signal. The SNR compares the ranging code with a pre-programmed satellite identity code of a corresponding satellite. The SNR detects cross correlation when the code comparison results in a mismatch and discards the navigation signal with the mismatched ranging code.