My question is that how it can be ensured that methyl jasmonate treatment works well? How we can demonstrate the activation of methyl jasmonate response at morphological, physiological and molecular level in treated plants?
What is your final aim for using MJ? is it elicitation, as generally it is being used for that. If so than simply analyzing metabolite content can be a parametre. Its application will also affect the growth of plant. There are many literatures available for the same as it is very well worked elicitor.
There are many JA-responsive gene markers, such as AOS (JA biosynthesis gene) among others, which are activated upon MeJA treatment trough a positive feeback loop. Consequently, you could test the expression of AOS using qRT-PCR and you would expect to see induced transcript level(s).
Depending on the MeJA concentration and treatment duration used, as well as the plant you work on, simple physiological observations such as anthocyanin production (pink-ish colouring of petioles) could be made. At least this is usually the case in Arabidopsis thaliana.