Novel hydrogels were prepared starting from different cellulose allomorphs (cellulose I, II, and III), through a swelling stage in 8.5% NaOH aqueous solution, followed by freezing at low temperature (−30 °C), for 24 h. After thawing at room temperature, the obtained gels were chemical cross-linked with epichlorohydrin (ECH), at 85 °C. The swelling degrees of the hydrogels were investigated, and a complex dependence on the type of the cellulose allomorph was found. Moreover, the gel stage has been shown to play a key role in the design of hydrogels with different performances, following the series: H-CII > H-CI > H-CIII. The correlations between the allomorph type and the morphological characteristics of hydrogels were established by scanning electron microscopy (SEM). The hydrogel H-CII showed the biggest homogeneous pores, while H-CIII had the most compacted pores network, with small interconnected pores. The rheological studies were performed in similar shear regimes, and a close correlation between the strength of the gel structure and the size of the gel fragments was observed. In the case of hydrogels, it has been shown that H-CII is softer, with a lower resistance of the hydrogel (G′) above the oscillation frequencies tested, but it maintains its stable structure, while H-CIII has the highest modulus of storage and loss compared to H-CI and H-CII, having a stronger and more rigid structure. The X-ray diffraction (XRD) method showed that the crystalline organization of each type of allomorph possesses a distinctive diffraction pattern, and, in addition, the chemically cross-linking reaction has been proved by a strong decrease of the crystallinity. Attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy provided clear evidence of the chemical cross-linking of cellulose allomorphs with ECH, by the alteration of the crystal structure of cellulose allomorphs and by the formation of new ether bands.