The recent IceCube detection of significant neutrino flux from the inner Galactic plane has provided us valuable insights on the spectrum of cosmic rays in our Galaxy. This flux can be produced either by a population of Galactic point sources or by diffused emission from cosmic ray interactions with the interstellar medium or by a mixture of both. In this work, we compute diffused gamma-ray and neutrino fluxes produced by a population of giant molecular clouds (GMCs) in our Galaxy, assuming different parametrizations of the Galactic diffused cosmic ray distribution. In particular, we take into account two main cases: (I) constant cosmic ray luminosity in our Galaxy, and (II) space-dependent cosmic ray luminosity, based on the supernovae distribution in our Galaxy. For Case-I, we found that the neutrino flux from GMCs is a factor of ∼ 10 below compared to π 0 and KRA γ best-fitted models of IceCube observations at 105 GeV. Instead, for Case-II the model can explain up to ∼ 90 % of the neutrino flux at that energy. Moreover, for this last scenario IceCube detector could be able to detect neutrino events from the Galactic centre regions. We then calculated gamma-ray and neutrino fluxes from individual GMCs and noticed that several current and future Cherenkov telescopes and neutrino observatories have the right sensitivities to study these objects. In particular, very neutrino-bright region such as Aquila Rift is favourable for detection by the IceCube-Gen2 observatory.