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The neuron connections in the central nervous system play an important role in the structure of the life organ. The neurons control the operational mechanism of an entire brain which sways the intact system of the body. An itty bitty variation of neurons in the brain creates a serious complication which may lead to the brain haemorrhage. The amount of the variation/deformation of neuron in brain determines the stage of the brain stroke. So an early computation of the deformation of neuron saves from brain haemorrhage. Keeping the importance of the neuron deformation in the brain, the present article employs one dimensional photonic structure to fetch the amount of deformation in the brain using infrared (IR) signal of 1310 nm (wavelength). The principle of measurement of the deformation relies on the light transmittance characteristics of three layers of photonic structure which contains the tissues of the brain. The output power emerging from one dimensional photonic structure indicates the status of the neuron deformation. The output result infers that the amount of deformation of the of neuron decreases linearly with the increasing of an output power. Same techniques are applied for both focusing clear and CLARITY specimen for the sake of validation. For example; the outcomes of the same specify that the output power decreases from 23.9923 µW to 0.0076 µW for deformation raging from 1.0 µm to 1.4 µm of the brain from CLARITY. Similarly, the output power decreases from 29.1294 µW to 0.27956 µW for deformation raging from 1.0 µm to 1.4 µm of the brain from focus clear method. To sum up, the outcomes of the current research confirms that the amount of the deformation in the brain can be identified by knowing the output power. In short, the present work proposes a photonic crystal based sensor through which one can fetch the amount deformation of the brain by knowing the amount of transmitted signal at the output end. For example; the neuron deformation which is ranging from 1.0 µm to 1.4 µm could be known instantly by applying 1310 nm to the proposed photonic structure.