Phosphorus magnetic resonance spectroscopy imaging (31P-MRSI) allows the probing of biological compounds that hold fundamental cellular information. High resolution MRSI at 3T suffers from low signal-to-noise ratio (SNR) inherent to the nuclear low sensitivity. This is accentuated in the MRSI in comparison to unlocalized free induction decay (FID) where acquired volumes are smaller and consequently lower the SNR. Our Convolutional Neural Network (CNN) based algorithm perform efficient quantification of metabolite and is compared to last-square fitting algorithm. Our model was trained with a simulated dataset and tested with both simulated spectra and real spectra from 3D 31P-MRSI acquired in kidneys.