The moisture concentration in mycelial block is an important factor for increasing the yield of high-quality shiitake mushrooms (Lentinula edodes) with a pileus of 4–5cm or more in mycelial block cultivation. Here, we show a novel way to measure moisture concentration in mycelial blocks using magnetic resonance imaging (MRI). The culture medium was inoculated with Hokken No. 607 and mycelial blocks were incubated and their moisture concentration was measured using MRI. A method was developed to calculate the spatial distribution of moisture concentration inside the mycelial blocks by measuring the total water mass in the mycelial block using mass method and creating a calibration line. During the maturation phase of the mycelial block (46–98 days of incubation), the moisture concentration in the top region of the mycelial block decreased once at 66 days of incubation and then gradually increased. The increase in moisture concentration was due to mycelia decomposing the culture medium and producing water. During the growth period of the fruiting body, the moisture concentration in the periphery of the fruiting body increased and, conversely, the moisture concentration in the whole mycelial block decreased because water in the mycelial block moved into the fruiting body.