In this research, we have extracted the covariant form of the Schrödinger equation in the Riemannian manifold
0.25emscriptM0.25em= ℝ3 with a position‐dependent mass (PDM) distribution in the presence of magnetic fields for each point
p∈scriptM. Then, we have solved the extracted nonrelativistic equation for a charged particle with a PDM in quantum system under the magnetic and Aharonov–Bohm (AB) flux fields and Yukawa‐like potential using the Frobenius series method. It is interesting that the obtained analytical solutions of the nonrelativistic equation have been expressed in terms of the biconfluent Heun function (BHF). Then, we have expanded the BHF as the power series and obtained a three‐term recurrence relation between the successive coefficients of the power expansion. To investigate the nontrivial solution of the power expansion, we need to apply an explicit continued fraction equation for the coefficients of the recurrence relation. This relation must be satisfied in order to assure the series convergence. At the continuation, we have found two different conditions using the submitted lemmas. Then, using the obtained conditions, we have calculated the eigenvalues and eigenfunctions of the particle in the arbitrary point of the manifold. Finally, the canonical formalism is applied to compute different thermodynamic variables for the case of the higher temperatures. Also, we have discussed the special states on the obtained results.