Rich hidden unconventional orders with pseudogap formation, such as the inter-site bond-order (BO), attract increasing attention in condensed matter physics. Here, we investigate the hidden order formation in organic unconventional superconductor $kappa$-(BEDT-TTF)$_2$X. We predict the formation of $d$-wave BO at wavelength $q=Q_B=(delta,delta)$ ($delta=0.38pi$) for the first time, based on both the functional renormalization group (fRG) and the density-wave equation theories. The origin of the BO is the quantum interference among antiferromagnetic spin fluctuations. This prediction leads to distinct pseudogap-like reduction in the NMR $1/T_1$ relaxation rate and in the density-of-states, consistently with essential experimental reports. The present theory would be applicable for other strongly correlated metals with pseudogap formation.