•Holmium and Erbium doped KTiOPO4 crystals were grown by a top-seeded solution growth method.•Transparent KTP:Ho and KTP:Er crystal were obtained from the mixed K6P4O13 solvent containing MoO3.•The doping of Ho and Er into KTP can alters the TiO6 network in the crystal.•The structural analysis of Ho and Er:KTP crystals were analyzed using Raman Shift and Electron Spin Resonance (ESR) Spectrum.•The characteristic SHG emission was analyzed. KTiOPO4:Ho and KTiOPO4:Er single crystals are grown by a top-seeded solution growth method from potassium phosphate and MoO3 flux. The crystalline phase, packing structure and chemical composition of the crystals are analyzed by X-ray diffraction (XRD), energy dispersive spectrum (EDS). The doping of Ho and Er induced strain in the crystal is determined from Williamson–Hall relation. The bonding between titanium and oxygen of Ho and Er doping in the KTP crystal is changing the pseudo-symmetrical deviation in the lattice. The bonding of O and Ti decreases with doping Ho and Er and Ti3+ content in the crystal. The bonding, distortion of the TiO6-TiO6 chain and change in inter-atomic distances by erbium and holmium doping are assessed by Raman spectroscopy and low temperature ESR spectroscopy which evidences the low concentration of Ti3+ presence in the crystal. The KTiOPO4:Ho and KTiOPO4:Er single crystal shows second harmonic generation properties which shows that the efficiency ratio of ηKTiOPO4:Ho/η KTiOPO4 = 0.63 and ηKTiOPO4:Er/η KTiOPO4 = 0.80.