For sustainable food production, labor-saving cultivation systems are required. Yam, a major food crop, is cultivated mostly with supports such as stakes (staking), which increases tuber yield (TY) but involves high material and labor costs. We, therefore, focused on non-staking water yam cultivation, in which no stakes are used. The effects of different cultivation methods (staking vs. non-staking) on TY, yield components, shoot traits, and tuber shape of six cultivars were investigated in a two-year field experiment, and phenotypic traits related to yielding ability in non-staking cultivation were analyzed. Averaged across years and cultivars, TY was significantly lower (by 19%) in non-staking than in staking cultivation because of smaller single-tuber weight. TY was significantly affected by the cultivation × cultivar interaction. We found no difference among cultivars in staking cultivation. In non-staking cultivation, Yamatomakousha and Shirokoushaman 1 cultivars had higher TY than the other cultivars, which was similar to their TY in staking cultivation. Shoot dry weight and vine number were closely associated with TY in both cultivations, whereas lower tuber length-to-width ratio was strongly related to higher TY only in non-staking. Tubers of Yamatomakousha and Shirokoushaman 1 were more rounded than those of other cultivars. In non-staking cultivation, these two cultivars showed a higher vine number and, thus, maintained higher TY owing to higher above-ground growth. Therefore, rounded tubers and high vine number are target traits for non-staking cultivation of water yam.