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I have created a executable file using Matlab which runs using MCR but it takes more time in comparison to Matlab command terminal.

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    You aren't doing a fair comparison. You should compare the MCR executable to "starting MATLAB and executing the code"... Commented Aug 7, 2015 at 10:41

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If you start the executable the first time, the MATLAB runtime is being loaded that can take some seconds. If you start it a second time the runtime should be cached in the RAM and it should run faster like within MATLAB.

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I am measuring execution time using following commands echo %time% myApp.exe and saving these commands in a batch file named Myexe.bat and ran this batch file using command prompt in windows.
D:\codes\Matlab>Myexe.bat D:\codes\Matlab>echo 13:04:06.91 13:04:06.91 D:\codes\Matlab>myApp.exe 11-Aug-2015 13:05:26 Elapsed time is 12.705512 seconds. It is taking almost 80 seconds to run actual program after invocation of exe file.

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