Isotope effects have been investigated in Neutral Beam Injection (NBI) heated plasmas on the Large Helical Device with similar operational parameters between Hydrogen (H) and Deuterium (D) plasmas. Experimental results show that the global energy confinement has no significant dependence on the isotope mass under similar discharge conditions with nearly the same heating power, line-averaged density ( nˉe ) and magnetic field. For both electron and ion energy transport, the transport coefficients, which are obtained based on local power balance analysis, have analogous profiles between H and D dominant plasmas. For neoclassical χe and χi values, they are almost equal between H and D dominant plasmas in low nˉe discharges, whereas in high nˉe cases they are lower in H plasmas than those in D ones. At low nˉe , the electron and ion thermal transport in both H and D plasmas are dominated by neoclassical transport at a certain zone ( ρ≈0.6−0.85 ), while the anomalous transport process has primary effects in the remaining area, and the density fluctuations exhibit ion temperature gradient mode nature. With increase of nˉe , the anomalous transport becomes prevailing and the density fluctuations propagate along electron diamagnetic drift direction. Bispectral analysis reveals that the H plasma has stronger nonlinear coupling in edge density fluctuations in both low and high density discharges, which is probably due to that the D plasma has stronger damping rate for the nonlinear interaction of turbulence. For a comparative study, the present results have been compared with those observed in the ECRH discharges (Tanaka et al 2019 Nucl. Fusion 59 126040). The reasons for the similarities and dissimilarities between these two different heating manners are not clear yet. To unravel the underlying physics, essential inputs from theories and simulations are required.