Holographic tomography (HT) is a measurement technique utilizing refractive index (RI) as imaging contrast and enabling wide spectrum of applications in modern cell biology. Obtained 3D RI distribution within a sample is quantitative, however it is prone to phase measurement and numerical errors especially in the case of limited angle holographic tomography (LATH). Therefore, determination and control over metrological parameters of HT system is crucial for credibility and usefulness of obtained results. In this work we propose a new type of calibration 3D phantom for LATH that allows to determine accuracy of a tomographic system. We have experimentally verified that it is possible to design, fabricate (using two-photon polymerization method) and measure complex microstructure containing regions of constant, step-like and gradient RI distribution. The phantom printing parameters required to obtain the reference RI values are determined based on its measurements using well-established 2D techniques (digital holographic microscope and white-light interferometry). The final calibration structure printed with multiple RI levels is measured by full angle HT as the reference method for LAHT. The advantages and limitations connected with implementation of the proposed phantom are discussed.