In multiple-eigenvalue modulated nonlinear frequency division multiplexing (NFDM) systems, the noise degrades the accuracy of the nonlinear Fourier transform (NFT) algorithm, resulting in perturbations in the received eigenvalues and the corresponding discrete spectrum. Moreover, with the increase in the number of eigenvalues and the order of the modulation formats, the impact of noise on the performance of the system is even more. A noise equalization scheme based on complex-valued artificial neural network (c-ANN) for multiple-eigenvalue modulated NFDM systems is proposed. This sceheme inputs the eigenvalues perturbation and the impaired discrete spectrum corresponding to the eigenvalues into the c-ANN in complex form. The scheme constructs a complex-valued logic structure with both amplitude and phase information, overlapping reuse input features and, thereby, effectively reducing the effect of noise on the multiple-eigenvalue NFDM system. The effectiveness of the scheme is verified in long-haul seven-eigenvalue modulated single-polarization NFDM simulation systems with 1 GBaud 16APSK/16QAM/64APSK/64QAM modulation formats, and the results show that the scheme outperforms the NFT receiving without equalization by 1 to 2 orders of magnitude in terms of bit error rate (BER). Among them, the transmission distance of the 64APSK signal after equalization exceeds 800 km while the BER meets 7% forward error correction (FEC) threshold, which is 600 km longer than that of the disequilibrium case, and the spectral efficiency (SE) can reach 1.85 bit/s/Hz. Compared with other schemes, the proposed scheme has better equalization performance under the same complexity, and the complexity can be reduced by half or even under the same performance.