Clayey soil, widely distributed in the Hokuriku region, Japan, is unsuitable for upland crop cultivation. Continuous upland cropping improves soil pore distribution. However, the practice of puddling for rice cultivation disrupts it considerably. We investigated changes in the topsoil pore distribution of a clayey field in a heavy-snowfall region in a 2-year triple cropping system of puddled rice–barley–soybean over 4 years. As straw can be applied during paddy cultivation to counter the decline in soil fertility during the use of paddy fields as upland fields, we investigated its effects on pore distribution and C and N contents. Macropore content increased from 0.03 m3 m−3 after the first rice crop to 0.30 m3 m−3 after soybean cultivation but declined to 0.03 m3 m−3 after the second rice crop. Conversely, residual water-holding pore content decreased from 0.5 m3 m−3 after the first rice crop to 0.3 m3 m−3 after soybean cultivation but increased again to 0.5 m3 m−3 after the second rice crop. Bulk density measured approximately 1.1 Mg m−3 after rice and barley cultivation but 0.8 Mg m−3 after the soybean crop. Readily available water-holding pore content remained stable at around 0.07 m3 m−3 over 4 years. Straw application exerted no significant effect on pore distribution. During the growth of upland crops, the pore distribution became gradually more suitable for upland use, but puddling for rice completely disturbed it again. Total C and N content decreased significantly during the cropping period, although available N content remained unchanged. However, straw application significantly mitigated these declines.