Recently, the gamma-ray telescopes AGILE and Fermi observed several middle-aged supernova remnants (SNRs) interacting with molecular clouds. A plausible emission mechanism of the gamma-rays is the decay of neutral pions produced by cosmic ray (CR) nuclei (hadronic processes). However, observations do not rule out contributions from bremsstrahlung emission due to CR electrons. TeV gamma-ray telescopes also observed many SNRs and discovered many unidentified sources. It is still unclear whether the TeV gamma-ray emission is produced via leptonic processes or hadronic processes. In this Letter, we propose that annihilation emission of secondary positrons produced by CR nuclei is a diagnostic tool of the hadronic processes. We investigate MeV emissions from secondary positrons and electrons produced by CR protons in molecular clouds. The annihilation emission of the secondary positrons from SNRs can be robustly estimated from the observed gamma-ray flux. The expected flux of the annihilation line from SNRs observed by AGILE and Fermi is sufficient for the future Advanced Compton Telescope to detect. Moreover, synchrotron emission from secondary positrons and electrons and bremsstrahlung emission from CR protons can be also observed by the future X-ray telescope NuSTAR and Astro-H.